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Fluorescent & tool proteins (PDB): 81 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.

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Luciferase and Green Fluorescent Protein from Renilla Reniformis — Crystal structures of the luciferase and green fluorescent protein from renilla reniformis — X-ray structure, 2007 (PDB 2RH7), downloaded from the RCSB Protein Data Bank.
Discosoma Red Fluorescent Protein (DsRed) Variant Q66M — Crystal structure of the discosoma red fluorescent protein (dsred) variant q66m — X-ray structure, 2005 (PDB 1ZGQ), downloaded from the RCSB Protein Data Bank.
RsFolder in the non-fluorescent off-state — Crystal structure of rsfolder in the non-fluorescent off-state — X-ray structure, 2016 (PDB 5DU0), downloaded from the RCSB Protein Data Bank.
A non-cytotoxic DsRed variant for whole-cell labeling — A non-cytotoxic dsred variant for whole-cell labeling — X-ray structure, 2008 (PDB 2V4E), downloaded from the RCSB Protein Data Bank.
Green Fluorescent Protein Mutant F99S, M153T and V163A — Green fluorescent protein mutant f99s, m153t and v163a — X-ray structure, 2000 (PDB 1B9C), downloaded from the RCSB Protein Data Bank.
SfGFP double mutant - 133/149 p-cyano-L-phenylalanine — sfgfp double mutant - 133/149 p-cyano-l-phenylalanine — X-ray structure, 2016 (PDB 5DPI), downloaded from the RCSB Protein Data Bank.
Green-fluorescent variant of the non-fluorescent chromoprotein Rtms5 — Green-fluorescent variant of the non-fluorescent chromoprotein rtms5 — X-ray structure, 2012 (PDB 3VIC), downloaded from the RCSB Protein Data Bank.
Three-dimensional structure of bacterial luciferase from vibrio… — Three-dimensional structure of bacterial luciferase from vibrio harveyi at 2.4 angstroms resolution — X-ray structure, 1996 (PDB 1BRL), downloaded from the RCSB Protein Data Bank.
Bacterial luciferase — Bacterial luciferase — X-ray structure, 1996 (PDB 1LUC), downloaded from the RCSB Protein Data Bank.
Luciferase domain from the dinoflagellate Lingulodinium polyedrum — Crystal structure of a luciferase domain from the dinoflagellate lingulodinium polyedrum — X-ray structure, 2005 (PDB 1VPR), downloaded from the RCSB Protein Data Bank.
Bacterial luciferase BETA2 homodimer — Bacterial luciferase beta2 homodimer — X-ray structure, 1997 (PDB 1XKJ), downloaded from the RCSB Protein Data Bank.
Alkanal monooxygenase beta chain — Structure of alkanal monooxygenase beta chain — X-ray structure, 1997 (PDB 1BSL), downloaded from the RCSB Protein Data Bank.
LuxB from Photobacterium leiognathi — Structure of luxb from photobacterium leiognathi — X-ray structure, 2018 (PDB 6FRI), downloaded from the RCSB Protein Data Bank.
Bacterial Luciferase:Flavin Complex Reveals the Basis of… — Crystal structure of the bacterial luciferase:flavin complex reveals the basis of intersubunit communication — X-ray structure, 2009 (PDB 3FGC), downloaded from the RCSB Protein Data Bank.
Homodimeric luciferase from Enhygromyxa salina — Structure of homodimeric luciferase from enhygromyxa salina — X-ray structure, 2024 (PDB 8CBB), downloaded from the RCSB Protein Data Bank.
BdsA from Bacillus subtilis WU-S2B — Crystal structure of bdsa from bacillus subtilis wu-s2b — X-ray structure, 2017 (PDB 5TLC), downloaded from the RCSB Protein Data Bank.
Apo-core-streptavidin in complex with biotin (two unoccupied binding… — Apo-core-streptavidin in complex with biotin (two unoccupied binding sites) at ph 4.5 — X-ray structure, 1998 (PDB 1SWD), downloaded from the RCSB Protein Data Bank.
Apo-core-streptavidin in complex with biotin at ph 4.5 — Apo-core-streptavidin in complex with biotin at ph 4.5 — X-ray structure, 1998 (PDB 1SWE), downloaded from the RCSB Protein Data Bank.
Core-streptavidin mutant W79F in complex with biotin at ph 4.5 — Core-streptavidin mutant w79f in complex with biotin at ph 4.5 — X-ray structure, 1999 (PDB 1SWK), downloaded from the RCSB Protein Data Bank.
Core-streptavidin mutant W120F in complex with biotin at ph 7.5 — Core-streptavidin mutant w120f in complex with biotin at ph 7.5 — X-ray structure, 1999 (PDB 1SWP), downloaded from the RCSB Protein Data Bank.
Streptavidin Mutant N23A with biotin at 1.89A — Streptavidin mutant n23a with biotin at 1.89a — X-ray structure, 2003 (PDB 1N43), downloaded from the RCSB Protein Data Bank.
Streptavidin Mutant S27A with Biotin at 1.6A Resolution — Streptavidin mutant s27a with biotin at 1.6a resolution — X-ray structure, 2003 (PDB 1N9M), downloaded from the RCSB Protein Data Bank.
Streptavidin Mutant Y43F with Biotin at 1.81A Resolution — Streptavidin mutant y43f with biotin at 1.81a resolution — X-ray structure, 2003 (PDB 1NDJ), downloaded from the RCSB Protein Data Bank.
Streptavidin Double Mutant S45A/D128A with Biotin: Cooperative… — Crystal structure of streptavidin double mutant s45a/d128a with biotin: cooperative hydrogen-bond interactions in the streptavidin-biotin system. — X-ray structure, 2003 (PDB 1MEP), downloaded from the RCSB Protein Data Bank.
SNAP-tag bound to its substrate benzylguanine — Crystal structure of snap-tag bound to its substrate benzylguanine — X-ray structure, 2010 (PDB 3KZZ), downloaded from the RCSB Protein Data Bank.
Benzylated SNAP-tag — Crystal structure of benzylated snap-tag — X-ray structure, 2010 (PDB 3L00), downloaded from the RCSB Protein Data Bank.
SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore — Crystal structure of snap-tag labeled with a benzyl-tetramethylrhodamine fluorophore — X-ray structure, 2021 (PDB 6Y8P), downloaded from the RCSB Protein Data Bank.
SNAP-tag — Crystal structure of snap-tag — X-ray structure, 2010 (PDB 3KZY), downloaded from the RCSB Protein Data Bank.
Haloalkane dehalogenase HOB (HaloTag7-based Oligonucleotide Binder)… — X-ray structure of the haloalkane dehalogenase hob (halotag7-based oligonucleotide binder) labeled with a chloroalkane-tetramethylrhodamine fluorophore substrate — X-ray structure, 2021 (PDB 6ZCC), downloaded from the RCSB Protein Data Bank.
Haloalkane dehalogenase HaloTag7 labeled with a… (6Y7A) — X-ray structure of the haloalkane dehalogenase halotag7 labeled with a chloroalkane-tetramethylrhodamine fluorophore substrate — X-ray structure, 2021 (PDB 6Y7A), downloaded from the RCSB Protein Data Bank.
Haloalkane dehalogenase HaloTag7 labeled with a… (6Y7B) — X-ray structure of the haloalkane dehalogenase halotag7 labeled with a chloroalkane-carbopyronine fluorophore substrate — X-ray structure, 2021 (PDB 6Y7B), downloaded from the RCSB Protein Data Bank.
Type II-C Cas9 enzyme from Actinomyces naeslundii — Crystal structure of the type ii-c cas9 enzyme from actinomyces naeslundii — X-ray structure, 2014 (PDB 4OGC), downloaded from the RCSB Protein Data Bank.
Nuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) — Nuclease-inactive streptococcus pyogenes cas9 (d10a/h840a, dcas9) in complex with single-guide rna at 3.1 angstrom resolution — X-ray structure, 2015 (PDB 4ZT9), downloaded from the RCSB Protein Data Bank.
DCas9 bound to on-target EMX1-1 (-)SC DNA minicircle — dcas9 bound to on-target emx1-1 (-)sc dna minicircle — Cryo-EM structure, 2026 (PDB 9H4J), downloaded from the RCSB Protein Data Bank.
Cas9 in complex with 12-14MM DNA substrate, 5 minute time-point — Cryo-em structure of cas9 in complex with 12-14mm dna substrate, 5 minute time-point — Cryo-EM structure, 2022 (PDB 7S4U), downloaded from the RCSB Protein Data Bank.
SuperFi Cas9 - mismatch 22nt sgRNA - DNA ternary complex class1 — Superfi cas9 - mismatch 22nt sgrna - dna ternary complex class1 — Cryo-EM structure, 2025 (PDB 9K4E), downloaded from the RCSB Protein Data Bank.
SuperFi Cas9 - mismatch 22nt sgRNA - DNA ternary complex class2 — Superfi cas9 - mismatch 22nt sgrna - dna ternary complex class2 — Cryo-EM structure, 2025 (PDB 9K4F), downloaded from the RCSB Protein Data Bank.
XCas9 P411T — Crystal structure of xcas9 p411t — X-ray structure, 2022 (PDB 7VK9), downloaded from the RCSB Protein Data Bank.
Inactivate TOD6 with TC DNA substrate — Inactivate tod6 with tc dna substrate — Cryo-EM structure, 2025 (PDB 9LCY), downloaded from the RCSB Protein Data Bank.
Inactivate TOD6 with CC DNA substrate — Inactivate tod6 with cc dna substrate — Cryo-EM structure, 2025 (PDB 9LD0), downloaded from the RCSB Protein Data Bank.
Inactivate TOD4 with TC DNA substrate — Inactivate tod4 with tc dna substrate — Cryo-EM structure, 2025 (PDB 9LD1), downloaded from the RCSB Protein Data Bank.
Inactive TOD6 with AC DNA substrate — Inactive tod6 with ac dna substrate — Cryo-EM structure, 2025 (PDB 9LCX), downloaded from the RCSB Protein Data Bank.
Inactivate TOD6 with GC DNA substrate — Inactivate tod6 with gc dna substrate — Cryo-EM structure, 2025 (PDB 9LCZ), downloaded from the RCSB Protein Data Bank.
Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore… — Cargo-loaded myxococcus xanthus enca encapsulin engineered pore mutant with t=3 icosahedral symmetry — Cryo-EM structure, 2024 (PDB 9B9Q), downloaded from the RCSB Protein Data Bank.
Cas9 bound to 12-14MM DNA, 60 min time-point, kinked conformation — Cas9 bound to 12-14mm dna, 60 min time-point, kinked conformation — Cryo-EM structure, 2022 (PDB 7S4V), downloaded from the RCSB Protein Data Bank.
Thermophilic O6-alkylguanine-DNA alkyltransferase-derived… — Crystal structure of a thermophilic o6-alkylguanine-dna alkyltransferase-derived self-labeling protein-tag in covalent complex with snap-vista green — X-ray structure, 2018 (PDB 6GA0), downloaded from the RCSB Protein Data Bank.
Extra-superfolder GFP — Extra-superfolder gfp — X-ray structure, 2017 (PDB 5B61), downloaded from the RCSB Protein Data Bank.
All-trans green fluorescent protein — Crystal structure of all-trans green fluorescent protein — X-ray structure, 2014 (PDB 4LW5), downloaded from the RCSB Protein Data Bank.
Mn-bound S.pyogenes Cas9 — Crystal structure of mn-bound s.pyogenes cas9 — X-ray structure, 2014 (PDB 4CMQ), downloaded from the RCSB Protein Data Bank.
Core-streptavidin mutant W108F in complex with biotin at ph 7.0 — Core-streptavidin mutant w108f in complex with biotin at ph 7.0 — X-ray structure, 1999 (PDB 1SWN), downloaded from the RCSB Protein Data Bank.
Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs… (9CJI) — Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 2 — Cryo-EM structure, 2025 (PDB 9CJI), downloaded from the RCSB Protein Data Bank.
Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs… (9CJJ) — Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 3 — Cryo-EM structure, 2025 (PDB 9CJJ), downloaded from the RCSB Protein Data Bank.
Cas12-1/crRNA complex — Cryo-em structure of cas12-1/crrna complex — Cryo-EM structure, 2025 (PDB 8WRT), downloaded from the RCSB Protein Data Bank.
Cas12-1 with 14 nt complementary heteroduplex — Cryo-em structure of cas12-1 with 14 nt complementary heteroduplex — Cryo-EM structure, 2025 (PDB 8WRQ), downloaded from the RCSB Protein Data Bank.
Cryo-EM mini structure of Cas12-1 with 14 nt complementary heteroduplex — Cryo-em mini structure of cas12-1 with 14 nt complementary heteroduplex — Cryo-EM structure, 2025 (PDB 8WS6), downloaded from the RCSB Protein Data Bank.
Cas12-1 with 10 nt complementary heteroduplex — Cryo-em structure of cas12-1 with 10 nt complementary heteroduplex — Cryo-EM structure, 2025 (PDB 8WRR), downloaded from the RCSB Protein Data Bank.
GFPuv complexed with the nanobody LaG16 at 1.67 Angstron resolution — Crystal structure of gfpuv complexed with the nanobody lag16 at 1.67 angstron resolution — X-ray structure, 2020 (PDB 6LR7), downloaded from the RCSB Protein Data Bank.
LaM2 Nanobody bound to mCherry — Crystal structure of lam2 nanobody bound to mcherry — X-ray structure, 2022 (PDB 7SAJ), downloaded from the RCSB Protein Data Bank.
Superfolder GFP bound to nanobody 15 — Structure of superfolder gfp bound to nanobody 15 — X-ray structure, 2026 (PDB 9ZG5), downloaded from the RCSB Protein Data Bank.
Nanobody in complex with eGFP — Nanobody in complex with egfp — X-ray structure, 2021 (PDB 6XZF), downloaded from the RCSB Protein Data Bank.
High Affinity nanobodies against GFP — High affinity nanobodies against gfp — X-ray structure, 2024 (PDB 8G0I), downloaded from the RCSB Protein Data Bank.
LaG16 Nanobody bound to eGFP — Crystal structure of lag16 nanobody bound to egfp — X-ray structure, 2022 (PDB 7SAH), downloaded from the RCSB Protein Data Bank.
Lag30 Nanobody bound to eGFP — Crystal structure of lag30 nanobody bound to egfp — X-ray structure, 2022 (PDB 7SAI), downloaded from the RCSB Protein Data Bank.
SfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution — Crystal structure of sfgfp complexed with the nanobody nb2 at 2.2 angstron resolution — X-ray structure, 2021 (PDB 7E53), downloaded from the RCSB Protein Data Bank.
LaM4 Nanobody bound to mCherry — Crystal structure of lam4 nanobody bound to mcherry — X-ray structure, 2022 (PDB 7SAK), downloaded from the RCSB Protein Data Bank.
Tobacco Etch Virus Protease C151A mutant — Crystal structure of the tobacco etch virus protease c151a mutant — X-ray structure, 2004 (PDB 1Q31), downloaded from the RCSB Protein Data Bank.
Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone… — Co-crystal structures of chikv nsp3 macrodomain with pyrimidone fragments — X-ray structure, 2021 (PDB 6W7H), downloaded from the RCSB Protein Data Bank.
Catalytically active tobacco etch virus protease complexed with product — Catalytically active tobacco etch virus protease complexed with product — X-ray structure, 2002 (PDB 1LVM), downloaded from the RCSB Protein Data Bank.
RNA-free helical (h8.5) virus-like particle composed of TEV coat protein — Rna-free helical (h8.5) virus-like particle composed of tev coat protein — Cryo-EM structure, 2026 (PDB 9R9W), downloaded from the RCSB Protein Data Bank.
Catalytically inactive tobacco etch virus protease — Catalytically inactive tobacco etch virus protease complexed with substrate — X-ray structure, 2002 (PDB 1LVB), downloaded from the RCSB Protein Data Bank.
Sugar transporter Oant_3817 from Ochrobactrum anthropi, target… — Crystal structure of sugar transporter oant_3817 from ochrobactrum anthropi, target efi-510528, with bound glucose — X-ray structure, 2014 (PDB 4R2B), downloaded from the RCSB Protein Data Bank.
Sugar transporter BL01359 from bacillus licheniformis, target… — Crystal structure of sugar transporter bl01359 from bacillus licheniformis, target efi-510856, in complex with stachyose — X-ray structure, 2014 (PDB 4RK9), downloaded from the RCSB Protein Data Bank.
BioSAS-TEVp (C151A, core) bound to TEV protease cleavage peptide — Biosas-tevp (c151a, core) bound to tev protease cleavage peptide — X-ray structure, 2025 (PDB 9N7Y), downloaded from the RCSB Protein Data Bank.
Asgard AtubA/B2 microtubule — Cryoem structure of asgard atuba/b2 microtubule — Cryo-EM structure, 2025 (PDB 9HXC), downloaded from the RCSB Protein Data Bank.
Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs… (9CJH) — Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 1 — Cryo-EM structure, 2025 (PDB 9CJH), downloaded from the RCSB Protein Data Bank.
Cryo-EM mini structure of Cas12-1/crRNA/Target DNA complex — Cryo-em mini structure of cas12-1/crrna/target dna complex — Cryo-EM structure, 2025 (PDB 8WS8), downloaded from the RCSB Protein Data Bank.
Cryo-EM mini structure of Cas12-1 with 10 nt complementary heteroduplex — Cryo-em mini structure of cas12-1 with 10 nt complementary heteroduplex — Cryo-EM structure, 2025 (PDB 8WS7), downloaded from the RCSB Protein Data Bank.
Cas12-2/crRNA/Target DNA complex — Cryo-em structure of cas12-2/crrna/target dna complex — Cryo-EM structure, 2025 (PDB 8WRU), downloaded from the RCSB Protein Data Bank.
Cas12-1 with 5 nt complementary heteroduplex — Cryo-em structure of cas12-1 with 5 nt complementary heteroduplex — Cryo-EM structure, 2025 (PDB 8WRS), downloaded from the RCSB Protein Data Bank.
Cas12-1 with 20 nt complementary heteroduplex — Cryo-em structure of cas12-1 with 20 nt complementary heteroduplex — Cryo-EM structure, 2025 (PDB 8WRP), downloaded from the RCSB Protein Data Bank.
Cas9:sgRNA:DNA (S. pyogenes) with 0 RNA:DNA base pairs… — Cas9:sgrna:dna (s. pyogenes) with 0 rna:dna base pairs, closed-protein/bent-dna conformation — Cryo-EM structure, 2022 (PDB 7S36), downloaded from the RCSB Protein Data Bank.