Library › DNA & Proteins › DNA, RNA & chromatin (PDB)

DNA, RNA & chromatin (PDB): 90 3D models

DNA, RNA, nucleic-acid drugs, gene editing, proteins and 300+ real PDB structures (real sizes 1–100 nm). Each one is a ready-made 3D model you can turn, recolour and place in a figure — open BioDioRama and type its name in the Library search.

Open the 3D Studio

Malaria parasite Nucleosome Assembly Protein (NAP) — Crystal structure of malaria parasite nucleosome assembly protein (nap) — X-ray structure, 2009 (PDB 3FS3), downloaded from the RCSB Protein Data Bank.
Nucleosome assembly protein from Plasmodium falciparum at 2.4 A… — Crystal structure of nucleosome assembly protein from plasmodium falciparum at 2.4 a resolution — X-ray structure, 2009 (PDB 3GYW), downloaded from the RCSB Protein Data Bank.
Nucleosome Assembly Protein 1 from Plasmodium knowlesi — Nucleosome assembly protein 1 from plasmodium knowlesi — X-ray structure, 2009 (PDB 3HFD), downloaded from the RCSB Protein Data Bank.
Nucleosome assembly protein S (PfNapS) from Plasmodium falciparum — Crystal structure of nucleosome assembly protein s (pfnaps) from plasmodium falciparum — X-ray structure, 2017 (PDB 5X7V), downloaded from the RCSB Protein Data Bank.
Nucleosome assembly protein from Plasmodium falciparum — Crystal structure of nucleosome assembly protein from plasmodium falciparum — X-ray structure, 2009 (PDB 3GYV), downloaded from the RCSB Protein Data Bank.
Ccp1 — Crystal structure of ccp1 — X-ray structure, 2016 (PDB 5GPL), downloaded from the RCSB Protein Data Bank.
Structural Insight into the Sequence-Dependence of Nucleosome… — Structural insight into the sequence-dependence of nucleosome positioning — X-ray structure, 2010 (PDB 3LEL), downloaded from the RCSB Protein Data Bank.
Human tfiia/tbp/dna complex — Human tfiia/tbp/dna complex — X-ray structure, 2003 (PDB 1NVP), downloaded from the RCSB Protein Data Bank.
Yeast Brf1-TBP-DNA ternary complex — Crystal structure of a yeast brf1-tbp-dna ternary complex — X-ray structure, 2003 (PDB 1NGM), downloaded from the RCSB Protein Data Bank.
Yeast TFIIA/TBP/TATA-box DNA Complex — Structure of a yeast tfiia/tbp/tata-box dna complex — X-ray structure, 2005 (PDB 1RM1), downloaded from the RCSB Protein Data Bank.
Yeast tfiia/tbp/dna complex (1YTF) — Yeast tfiia/tbp/dna complex — X-ray structure, 1996 (PDB 1YTF), downloaded from the RCSB Protein Data Bank.
SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter — Structure of snapc:tbp-tfiia-tfiib sub-complex bound to u5 snrna promoter — Cryo-EM structure, 2022 (PDB 7ZWC), downloaded from the RCSB Protein Data Bank.
SNAPc containing Pol II pre-initiation complex — Structure of snapc containing pol ii pre-initiation complex bound to u1 snrna promoter (oc) — Cryo-EM structure, 2022 (PDB 7ZXE), downloaded from the RCSB Protein Data Bank.
Designed zinc finger protein bound to DNA — Crystal structure of a designed zinc finger protein bound to dna — X-ray structure, 1997 (PDB 1MEY), downloaded from the RCSB Protein Data Bank.
Aart, a six finger zinc finger designed to recognize ANN triplets — Aart, a six finger zinc finger designed to recognize ann triplets — X-ray structure, 2006 (PDB 2I13), downloaded from the RCSB Protein Data Bank.
BAZ2A PHD zinc finger in complex with Fr 19 — Crystal structure of baz2a phd zinc finger in complex with fr 19 — X-ray structure, 2018 (PDB 6FI0), downloaded from the RCSB Protein Data Bank.
Human BAZ2A PHD zinc finger in the free form — Crystal structure of human baz2a phd zinc finger in the free form — X-ray structure, 2014 (PDB 4QF2), downloaded from the RCSB Protein Data Bank.
Human BAZ2A PHD zinc finger in complex with Fr23 — Crystal structure of human baz2a phd zinc finger in complex with fr23 — X-ray structure, 2018 (PDB 6FAP), downloaded from the RCSB Protein Data Bank.
Double C2H2 Zinc Finger Protein from a Hyperthermophilic Archaeal… — The structure of a double c2h2 zinc finger protein from a hyperthermophilic archaeal virus in the absence of dna — X-ray structure, 2010 (PDB 2WBT), downloaded from the RCSB Protein Data Bank.
BAZ2A PHD zinc finger in complex with H3 3-mer peptide — Crystal structure of baz2a phd zinc finger in complex with h3 3-mer peptide — X-ray structure, 2018 (PDB 6FHU), downloaded from the RCSB Protein Data Bank.
BAZ2A PHD zinc finger in complex with H3 10-mer AA mutant peptide — Crystal structure of baz2a phd zinc finger in complex with h3 10-mer aa mutant peptide — X-ray structure, 2018 (PDB 6FKP), downloaded from the RCSB Protein Data Bank.
Glycine riboswitch, unbound state — Crystal structure of glycine riboswitch, unbound state — X-ray structure, 2010 (PDB 3OX0), downloaded from the RCSB Protein Data Bank.
FMN riboswitch bound to riboflavin — Crystal structure of the fmn riboswitch bound to riboflavin. — X-ray structure, 2009 (PDB 3F4G), downloaded from the RCSB Protein Data Bank.
THF riboswitch bound to 7-deazaguanine — Structure of the thf riboswitch bound to 7-deazaguanine — X-ray structure, 2014 (PDB 4LVW), downloaded from the RCSB Protein Data Bank.
SAM-I riboswitch from T. tencongensis variant A94G apo form — Sam-i riboswitch from t. tencongensis variant a94g apo form — X-ray structure, 2010 (PDB 3IQP), downloaded from the RCSB Protein Data Bank.
THF riboswitch bound to 2,6-diaminopurine — Structure of the thf riboswitch bound to 2,6-diaminopurine — X-ray structure, 2014 (PDB 4LVZ), downloaded from the RCSB Protein Data Bank.
Structural analysis of a class I PreQ1 riboswitch aptamer in the… — Structural analysis of a class i preq1 riboswitch aptamer in the metabolite-free state. — X-ray structure, 2011 (PDB 3Q51), downloaded from the RCSB Protein Data Bank.
All-rna hammerhead ribozyme: a proposed mechanism for RNA catalytic… — The crystal structure of an all-rna hammerhead ribozyme: a proposed mechanism for rna catalytic cleavage — X-ray structure, 1996 (PDB 1MME), downloaded from the RCSB Protein Data Bank.
Hammerhead Ribozyme G12A mutant after cleavage — Hammerhead ribozyme g12a mutant after cleavage — X-ray structure, 2008 (PDB 2QUW), downloaded from the RCSB Protein Data Bank.
Junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution — Crystal structure of a junctionless all-rna hairpin ribozyme at 2.05 angstroms resolution — X-ray structure, 2007 (PDB 2OUE), downloaded from the RCSB Protein Data Bank.
Vanadate at the Active Site of a Small Ribozyme Suggests a Role for… — Vanadate at the active site of a small ribozyme suggests a role for water in transition-state stabilization — X-ray structure, 2007 (PDB 2P7E), downloaded from the RCSB Protein Data Bank.
Methionyl-tRNA synthetase from Pyrococcus abyssi — Methionyl-trna synthetase from pyrococcus abyssi — X-ray structure, 2004 (PDB 1RQG), downloaded from the RCSB Protein Data Bank.
Glutamyl-trna synthetase complexed with trna(glu) — Glutamyl-trna synthetase complexed with trna(glu). — X-ray structure, 2001 (PDB 1G59), downloaded from the RCSB Protein Data Bank.
Architectures of class-defining and specific domains of… — Architectures of class-defining and specific domains of glutamyl-trna synthetase — X-ray structure, 1995 (PDB 1GLN), downloaded from the RCSB Protein Data Bank.
Methionyl-trna synthetase from thermus thermophilus — Methionyl-trna synthetase from thermus thermophilus — X-ray structure, 1999 (PDB 1A8H), downloaded from the RCSB Protein Data Bank.
Caenorhabditis elegans NAP1 — Crystal structure of caenorhabditis elegans nap1 — X-ray structure, 2019 (PDB 6N2G), downloaded from the RCSB Protein Data Bank.
Transcription factor TFIIA as a single chain protein — Transcription factor tfiia as a single chain protein — X-ray structure, 2017 (PDB 5M4S), downloaded from the RCSB Protein Data Bank.
Ccp1 mutant — Crystal structure of ccp1 mutant — X-ray structure, 2016 (PDB 5GPK), downloaded from the RCSB Protein Data Bank.
Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter — Human tfiib-related factor 2 (brf2) and tbp bound to rpph1 promoter — X-ray structure, 2015 (PDB 4ROE), downloaded from the RCSB Protein Data Bank.
Human BAZ2A PHD zinc finger — Crystal structure of human baz2a phd zinc finger in complex with unmodified h3k4 histone peptide — X-ray structure, 2014 (PDB 4Q6F), downloaded from the RCSB Protein Data Bank.
Glycine riboswitch with two mutations — Crystal structure of glycine riboswitch with two mutations — X-ray structure, 2010 (PDB 3OXD), downloaded from the RCSB Protein Data Bank.
Glycine riboswitch with single mutation — Crystal structure of glycine riboswitch with single mutation — X-ray structure, 2010 (PDB 3OXB), downloaded from the RCSB Protein Data Bank.
FMN riboswitch bound to roseoflavin — Crystal structure of the fmn riboswitch bound to roseoflavin — X-ray structure, 2009 (PDB 3F4H), downloaded from the RCSB Protein Data Bank.
Inhibition of the hammerhead ribozyme cleavage reaction by… — Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of tb(iii) — X-ray structure, 1997 (PDB 359D), downloaded from the RCSB Protein Data Bank.
Capturing the structure of a catalytic RNA intermediate: RNA… (301D) — Capturing the structure of a catalytic rna intermediate: rna hammerhead ribozyme, mg(ii)-soaked — X-ray structure, 1997 (PDB 301D), downloaded from the RCSB Protein Data Bank.
Capturing the structure of a catalytic RNA intermediate: RNA… (300D) — Capturing the structure of a catalytic rna intermediate: rna hammerhead ribozyme, mn(ii)-soaked — X-ray structure, 1997 (PDB 300D), downloaded from the RCSB Protein Data Bank.
A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of… — A minimal, 'hinged' hairpin ribozyme construct solved with mimics of the product strands at 2.25 angstroms resolution — X-ray structure, 2007 (PDB 2P7D), downloaded from the RCSB Protein Data Bank.
Capturing the structure of a catalytic RNA intermediate: the… — Capturing the structure of a catalytic rna intermediate: the hammerhead ribozyme — X-ray structure, 1997 (PDB 299D), downloaded from the RCSB Protein Data Bank.
Crystal structures at 2.5 angstroms resolution of seryl-trna synthetase — Crystal structures at 2.5 angstroms resolution of seryl-trna synthetase complexed with two different analogues of seryl-adenylate — X-ray structure, 1994 (PDB 1SET), downloaded from the RCSB Protein Data Bank.
Yeast TFIIA/TBP/DNA complex (1NH2) — Crystal structure of a yeast tfiia/tbp/dna complex — X-ray structure, 2003 (PDB 1NH2), downloaded from the RCSB Protein Data Bank.
Thermus thermophilus glutamyl-tRNA synthetase — Crystal structure of thermus thermophilus glutamyl-trna synthetase complexed with trna(glu) and glutamol-amp. — X-ray structure, 2003 (PDB 1N78), downloaded from the RCSB Protein Data Bank.
Thermus thermophilus valyl-trna synthetase — Crystal structure of thermus thermophilus valyl-trna synthetase complexed with trna(val) and valyl-adenylate analogue — X-ray structure, 2003 (PDB 1IVS), downloaded from the RCSB Protein Data Bank.
Thermus thermophilus arginyl-trna synthetase — Thermus thermophilus arginyl-trna synthetase — X-ray structure, 2001 (PDB 1IQ0), downloaded from the RCSB Protein Data Bank.
Cocrystal structure of an anti-parallel DNA G-quadruplex and a… — Cocrystal structure of an anti-parallel dna g-quadruplex and a tetra-quinoline foldamer — X-ray structure, 2016 (PDB 5HIX), downloaded from the RCSB Protein Data Bank.
Hybrid G-quadruplex from Tetrahymena thermophila telomeric sequence (9E8E) — Hybrid g-quadruplex from tetrahymena thermophila telomeric sequence in complex with trisqo form 2 — X-ray structure, 2026 (PDB 9E8E), downloaded from the RCSB Protein Data Bank.
KRAS G-quadruplex G16T mutant — Kras g-quadruplex g16t mutant. — X-ray structure, 2020 (PDB 6N65), downloaded from the RCSB Protein Data Bank.
Tetramolecular RNA G-quadruplex in potassium — Crystal structure of a tetramolecular rna g-quadruplex in potassium — X-ray structure, 2015 (PDB 4XK0), downloaded from the RCSB Protein Data Bank.
Hybrid G-quadruplex from Tetrahymena thermophila telomeric sequence (9C73) — Hybrid g-quadruplex from tetrahymena thermophila telomeric sequence in complex with trisqo — X-ray structure, 2025 (PDB 9C73), downloaded from the RCSB Protein Data Bank.
A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex (3NZ7) — A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains — X-ray structure, 2010 (PDB 3NZ7), downloaded from the RCSB Protein Data Bank.
A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex (3NYP) — A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains — X-ray structure, 2010 (PDB 3NYP), downloaded from the RCSB Protein Data Bank.
A DNA G-quadruplex/i-motif hybrid (6TZQ) — A dna g-quadruplex/i-motif hybrid — X-ray structure, 2019 (PDB 6TZQ), downloaded from the RCSB Protein Data Bank.
A DNA G-quadruplex/i-motif hybrid (6TZR) — A dna g-quadruplex/i-motif hybrid — X-ray structure, 2019 (PDB 6TZR), downloaded from the RCSB Protein Data Bank.
RecBCD in complex with Chi-minus2 substrate — Cryo-em structure of the recbcd in complex with chi-minus2 substrate — Cryo-EM structure, 2020 (PDB 6T2U), downloaded from the RCSB Protein Data Bank.
RecBCD-DNA in complex with the phage protein Abc2 — Recbcd-dna in complex with the phage protein abc2 — Cryo-EM structure, 2022 (PDB 8B1T), downloaded from the RCSB Protein Data Bank.
RecBCD in complex with the phage protein gp5.9 — Recbcd in complex with the phage protein gp5.9 — Cryo-EM structure, 2022 (PDB 8B1R), downloaded from the RCSB Protein Data Bank.
RecBCD-DNA complex with docked RecBNuc and stabilized RecD — Cryo-em structure of recbcd-dna complex with docked recbnuc and stabilized recd — Cryo-EM structure, 2021 (PDB 7MR3), downloaded from the RCSB Protein Data Bank.
Rad60 SLD2 Ubc9 Complex — Rad60 sld2 ubc9 complex — X-ray structure, 2011 (PDB 3RCZ), downloaded from the RCSB Protein Data Bank.
HMms2-hUbc13 — Crystal structure of hmms2-hubc13 — X-ray structure, 2001 (PDB 1J7D), downloaded from the RCSB Protein Data Bank.
Human Mms2/Ubc13 L121G mutant — Crystal structure of a human mms2/ubc13 l121g mutant — X-ray structure, 2014 (PDB 4NR3), downloaded from the RCSB Protein Data Bank.
Human Mms2/Ubc13 D118G mutant — Crystal structure of a human mms2/ubc13 d118g mutant — X-ray structure, 2014 (PDB 4NRG), downloaded from the RCSB Protein Data Bank.
Complete initiation complex of RecBCD — Crystal structure of the complete initiation complex of recbcd — X-ray structure, 2009 (PDB 3K70), downloaded from the RCSB Protein Data Bank.
Tudor domain of human Histone-lysine N-methyltransferase SETDB1 — Crystal structure of tudor domain of human histone-lysine n-methyltransferase setdb1 — X-ray structure, 2008 (PDB 3DLM), downloaded from the RCSB Protein Data Bank.
NSD3 tandem PHD5-C5HCH domains — Crystal structure of nsd3 tandem phd5-c5hch domains — X-ray structure, 2013 (PDB 4GND), downloaded from the RCSB Protein Data Bank.
SETDB1 Tudor domain in complex with UNC6535 — Crystal structure of setdb1 tudor domain in complex with unc6535 — X-ray structure, 2023 (PDB 8G5E), downloaded from the RCSB Protein Data Bank.
NSD3-PWWP1 in complex with compound 5 — X-ray structure of nsd3-pwwp1 in complex with compound 5 — X-ray structure, 2019 (PDB 6G27), downloaded from the RCSB Protein Data Bank.
NSD3-PWWP1 in complex with compound 6 — X-ray structure of nsd3-pwwp1 in complex with compound 6 — X-ray structure, 2019 (PDB 6G29), downloaded from the RCSB Protein Data Bank.
PF3D7_1475600, a bromodomain from Plasmodium Falciparum — Crystal structure of pf3d7_1475600, a bromodomain from plasmodium falciparum — X-ray structure, 2014 (PDB 4NXJ), downloaded from the RCSB Protein Data Bank.
Analysis of bromodomain from Leishmania donovani — Crystal structure analysis of bromodomain from leishmania donovani complexed with bromosporine — X-ray structure, 2015 (PDB 5C4Q), downloaded from the RCSB Protein Data Bank.
Trypanosoma cruzi bromodomain BDF2 (TcCLB.506553.20) — Crystal structure of trypanosoma cruzi bromodomain bdf2 (tcclb.506553.20) — X-ray structure, 2019 (PDB 6NP7), downloaded from the RCSB Protein Data Bank.
First bromodomain (BD1) of human BRD2 bound to Ro3280 — Crystal structure of the first bromodomain (bd1) of human brd2 bound to ro3280 — X-ray structure, 2021 (PDB 7LAJ), downloaded from the RCSB Protein Data Bank.
Domain Swapped Bromodomain from Leishmania donovani — Domain swapped bromodomain from leishmania donovani — X-ray structure, 2016 (PDB 5FEA), downloaded from the RCSB Protein Data Bank.
Bromodomain of human BRD1 — Crystal structure of the bromodomain of human brd1 — X-ray structure, 2011 (PDB 3RCW), downloaded from the RCSB Protein Data Bank.
Bromodomain of Trypanosoma brucei BDF2 With IBET-151 — Bromodomain of trypanosoma brucei bdf2 with ibet-151 — X-ray structure, 2015 (PDB 4PKL), downloaded from the RCSB Protein Data Bank.
Bromodomain from Plasmodium falciparum bromodomain protein 1 — Crystal structure of the bromodomain from plasmodium falciparum bromodomain protein 1 — X-ray structure, 2021 (PDB 7M97), downloaded from the RCSB Protein Data Bank.
NSD3-PWWP1 in complex with compound 4 — X-ray structure of nsd3-pwwp1 in complex with compound 4 — X-ray structure, 2019 (PDB 6G25), downloaded from the RCSB Protein Data Bank.
NSD3-PWWP1 in complex with compound 3 — X-ray structure of nsd3-pwwp1 in complex with compound 3 — X-ray structure, 2019 (PDB 6G24), downloaded from the RCSB Protein Data Bank.
Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate… — Methyltransferase domain of human wolf-hirschhorn syndrome candidate 1-like protein 1 (whsc1l1) — X-ray structure, 2017 (PDB 5UPD), downloaded from the RCSB Protein Data Bank.
Analysis of hypothetical bromodomain Tb427.10.7420 from Trypanosoma… — Crystal structure analysis of hypothetical bromodomain tb427.10.7420 from trypanosoma brucei in complex with bromosporine — X-ray structure, 2015 (PDB 5CZG), downloaded from the RCSB Protein Data Bank.
Whsc1l1-pwwp2 — crystal structure of whsc1l1-pwwp2 — X-ray structure, 2015 (PDB 4RXJ), downloaded from the RCSB Protein Data Bank.
Refined crystal structure of the seryl-trna synthetase from thermus… — Refined crystal structure of the seryl-trna synthetase from thermus thermophilus at 2.5 angstroms resolution — X-ray structure, 1994 (PDB 1SRY), downloaded from the RCSB Protein Data Bank.