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Bacteria & antibiotics (PDB): 72 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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PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae… — Pbp2x from a highly penicillin-resistant streptococcus pneumoniae clinical isolate — X-ray structure, 2001 (PDB 1K25), downloaded from the RCSB Protein Data Bank.
Penicillin-binding protein 2X (PBP-2X) (1PMD) — Penicillin-binding protein 2x (pbp-2x) — X-ray structure, 1997 (PDB 1PMD), downloaded from the RCSB Protein Data Bank.
Penicillin-binding protein 2X (PBP-2X) (1QME) — Penicillin-binding protein 2x (pbp-2x) — X-ray structure, 2000 (PDB 1QME), downloaded from the RCSB Protein Data Bank.
Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex… (2ZC3) — Penicillin-binding protein 2x (pbp 2x) acyl-enzyme complex (biapenem) from streptococcus pneumoniae — X-ray structure, 2008 (PDB 2ZC3), downloaded from the RCSB Protein Data Bank.
Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex… (2ZC4) — Penicillin-binding protein 2x (pbp 2x) acyl-enzyme complex (tebipenem) from streptococcus pneumoniae — X-ray structure, 2008 (PDB 2ZC4), downloaded from the RCSB Protein Data Bank.
T.thermophila 60S ribosomal subunit in complex with initiation factor 6 — T.thermophila 60s ribosomal subunit in complex with initiation factor 6. — X-ray structure, 2014 (PDB 4V8P), downloaded from the RCSB Protein Data Bank.
Control of ribosomal subunit rotation by elongation factor G (4V9O) — Control of ribosomal subunit rotation by elongation factor g — X-ray structure, 2014 (PDB 4V9O), downloaded from the RCSB Protein Data Bank.
Complex containing domain 3 of CrPV IGR IRES RNA — Crystal structure of a complex containing domain 3 of crpv igr ires rna bound to the 70s ribosome. — X-ray structure, 2014 (PDB 4V84), downloaded from the RCSB Protein Data Bank.
Thermorubin in complex with the 70S ribosome from Thermus thermophilus — The structure of thermorubin in complex with the 70s ribosome from thermus thermophilus. — X-ray structure, 2014 (PDB 4V8A), downloaded from the RCSB Protein Data Bank.
Control of ribosomal subunit rotation by elongation factor G (4V9P) — Control of ribosomal subunit rotation by elongation factor g — X-ray structure, 2014 (PDB 4V9P), downloaded from the RCSB Protein Data Bank.
70S Ribosome translocation intermediate FA-3.6A containing… — 70s ribosome translocation intermediate fa-3.6a containing elongation factor efg/fusidic acid/gdp, mrna, and trna bound in the pe*/e state. — X-ray structure, 2014 (PDB 4V9L), downloaded from the RCSB Protein Data Bank.
Bacterial ribosome ram mutation G299A — Crystal structure of the bacterial ribosome ram mutation g299a. — X-ray structure, 2014 (PDB 4V97), downloaded from the RCSB Protein Data Bank.
70S ribosome bound with the Q253P mutant of release factor RF2 — Crystal structure of the 70s ribosome bound with the q253p mutant of release factor rf2. — X-ray structure, 2014 (PDB 4V9N), downloaded from the RCSB Protein Data Bank.
Shiga-like toxin complexed with its receptor — Shiga-like toxin complexed with its receptor — X-ray structure, 1999 (PDB 1BOS), downloaded from the RCSB Protein Data Bank.
Mutated shiga-like toxin b subunit (G62T) — Mutated shiga-like toxin b subunit (g62t) — X-ray structure, 2000 (PDB 1C48), downloaded from the RCSB Protein Data Bank.
G62T mutant of shiga-like toxin i b subunit — Structure of the g62t mutant of shiga-like toxin i b subunit — X-ray structure, 2000 (PDB 1CZG), downloaded from the RCSB Protein Data Bank.
Pertussis toxin-sugar complex as a model for receptor binding — The structure of a pertussis toxin-sugar complex as a model for receptor binding — X-ray structure, 1995 (PDB 1PTO), downloaded from the RCSB Protein Data Bank.
Mutated shiga-like toxin b subunit (D17E/W34A) — Mutated shiga-like toxin b subunit (d17e/w34a) complexed with receptor gb3 analogue — X-ray structure, 2000 (PDB 1D1K), downloaded from the RCSB Protein Data Bank.
Membrane protein from Pseudomonas aeruginosa — Crystal structure of a membrane protein from pseudomonas aeruginosa — X-ray structure, 2016 (PDB 5AZS), downloaded from the RCSB Protein Data Bank.
Vitelline membrane outer layer protein i (vmo-i): a folding motif… — Crystal structure of vitelline membrane outer layer protein i (vmo-i): a folding motif with homologous greek key structures related by an internal three-fold symmetry — X-ray structure, 1994 (PDB 1VMO), downloaded from the RCSB Protein Data Bank.
Drug-discharge outer membrane protein, OprM — Crystal structure of the drug-discharge outer membrane protein, oprm — X-ray structure, 2004 (PDB 1WP1), downloaded from the RCSB Protein Data Bank.
OprM channel in a non-symmetrical space group — Crystal structure of the oprm channel in a non-symmetrical space group — X-ray structure, 2009 (PDB 3D5K), downloaded from the RCSB Protein Data Bank.
Outer membrane protein OprG from Pseudomonas aeruginosa — Crystal structure of the outer membrane protein oprg from pseudomonas aeruginosa — X-ray structure, 2010 (PDB 2X27), downloaded from the RCSB Protein Data Bank.
TolC in complex with hexamminecobalt — Structure of tolc in complex with hexamminecobalt — X-ray structure, 2004 (PDB 1TQQ), downloaded from the RCSB Protein Data Bank.
BamABCDE complex, outer membrane beta barrel assembly machinery… — Bamabcde complex, outer membrane beta barrel assembly machinery entire complex — X-ray structure, 2016 (PDB 5D0O), downloaded from the RCSB Protein Data Bank.
Membrane complex — Structure of a membrane complex — X-ray structure, 2016 (PDB 5AYW), downloaded from the RCSB Protein Data Bank.
Multidrug Efflux pump AdeJ with TP-6076 bound — Multidrug efflux pump adej with tp-6076 bound — Cryo-EM structure, 2022 (PDB 7RY3), downloaded from the RCSB Protein Data Bank.
Cryo-EM co-structure of AcrB with the CU032 efflux pump inhibitor — Cryo-em co-structure of acrb with the cu032 efflux pump inhibitor — Cryo-EM structure, 2024 (PDB 9BFH), downloaded from the RCSB Protein Data Bank.
Cryo-EM co-structure of AcrB with the EPM35 efflux pump inhibitor — Cryo-em co-structure of acrb with the epm35 efflux pump inhibitor — Cryo-EM structure, 2024 (PDB 9BFM), downloaded from the RCSB Protein Data Bank.
Cryo-EM co-structure of AcrB with the CU232 efflux pump inhibitor — Cryo-em co-structure of acrb with the cu232 efflux pump inhibitor — Cryo-EM structure, 2024 (PDB 9BFN), downloaded from the RCSB Protein Data Bank.
TolC, YbjP, and AcrABZ complex — Structure of tolc, ybjp, and acrabz complex — Cryo-EM structure, 2025 (PDB 9V53), downloaded from the RCSB Protein Data Bank.
Multidrug Efflux pump AdeJ with Eravacycline bound — Multidrug efflux pump adej with eravacycline bound — Cryo-EM structure, 2021 (PDB 7M4P), downloaded from the RCSB Protein Data Bank.
AcrBZ in complex with antibiotic puromycin — Crystal structure of acrbz in complex with antibiotic puromycin — X-ray structure, 2017 (PDB 5NC5), downloaded from the RCSB Protein Data Bank.
Thermus thermophilus Rod shape determining protein RodA D255A mutant… — Crystal structure of thermus thermophilus rod shape determining protein roda d255a mutant (q5six3_thet8) — X-ray structure, 2018 (PDB 6BAS), downloaded from the RCSB Protein Data Bank.
Structural coordination of polymerization and crosslinking by a… (6PL5) — Structural coordination of polymerization and crosslinking by a peptidoglycan synthase complex — X-ray structure, 2020 (PDB 6PL5), downloaded from the RCSB Protein Data Bank.
Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex — Structural basis of peptidoglycan synthesis by e. coli roda-pbp2 complex — Cryo-EM structure, 2023 (PDB 8TJ3), downloaded from the RCSB Protein Data Bank.
Manduca sexta Peptidoglycan Recognition Protein-1 — Manduca sexta peptidoglycan recognition protein-1 — X-ray structure, 2019 (PDB 6CKH), downloaded from the RCSB Protein Data Bank.
Type I pilus from enterotoxigenic Escherichia coli — Cryo-em structure of the type i pilus from enterotoxigenic escherichia coli — Cryo-EM structure, 2025 (PDB 9IUG), downloaded from the RCSB Protein Data Bank.
AdeG from Acinetobacter baumannii — Cryo-em structure of adeg from acinetobacter baumannii — Cryo-EM structure, 2025 (PDB 8YR0), downloaded from the RCSB Protein Data Bank.
Multidrug Efflux pump AdeJ — Multidrug efflux pump adej — Cryo-EM structure, 2021 (PDB 7M4Q), downloaded from the RCSB Protein Data Bank.
Thermus thermophilus Rod shape determining protein RodA (Q5SIX3_THET8) — Crystal structure of thermus thermophilus rod shape determining protein roda (q5six3_thet8) — X-ray structure, 2018 (PDB 6BAR), downloaded from the RCSB Protein Data Bank.
Antigenic outer membrane protein ST50 from Salmonella Typhi — Crystal structure of an antigenic outer membrane protein st50 from salmonella typhi — X-ray structure, 2015 (PDB 5BUN), downloaded from the RCSB Protein Data Bank.
70S ribosome translocation intermediate GDPNP-I containing… — 70s ribosome translocation intermediate gdpnp-i containing elongation factor efg/gdpnp, mrna, and trna bound in the pe*/e state. — X-ray structure, 2014 (PDB 4V9K), downloaded from the RCSB Protein Data Bank.
Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from… — Cefditoren-acylated penicillin-binding protein 2x (pbp2x) from streptococcus pneumoniae — X-ray structure, 2007 (PDB 2Z2M), downloaded from the RCSB Protein Data Bank.
Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae — Penicillin-binding protein 2x (pbp2x) from streptococcus pneumoniae — X-ray structure, 2007 (PDB 2Z2L), downloaded from the RCSB Protein Data Bank.
PBP2x from Streptococcus pneumoniae strain 5259 with reduced… — Pbp2x from streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics — X-ray structure, 2004 (PDB 1RP5), downloaded from the RCSB Protein Data Bank.
A mutant shiga-like toxin iie — A mutant shiga-like toxin iie — X-ray structure, 2000 (PDB 1QOH), downloaded from the RCSB Protein Data Bank.
Penicillin G acyl-Penicillin binding protein 2a from methicillin… — Structure of penicillin g acyl-penicillin binding protein 2a from methicillin resistant staphylococcus aureus strain 27r at 2.45 a resolution. — X-ray structure, 2002 (PDB 1MWT), downloaded from the RCSB Protein Data Bank.
W34A mutant of shiga-like toxin i b subunit — Structure of the w34a mutant of shiga-like toxin i b subunit — X-ray structure, 2000 (PDB 1CZW), downloaded from the RCSB Protein Data Bank.
Mutated shiga-like toxin b subunit (F30A/W34A) — Mutated shiga-like toxin b subunit (f30a/w34a) complexed with receptor gb3 analogue — X-ray structure, 2000 (PDB 1C4Q), downloaded from the RCSB Protein Data Bank.
Structural coordination of polymerization and crosslinking by a… (6PL6) — Structural coordination of polymerization and crosslinking by a peptidoglycan synthase complex — X-ray structure, 2020 (PDB 6PL6), downloaded from the RCSB Protein Data Bank.
ShyA endopeptidase from Vibrio cholera (open form) — Shya endopeptidase from vibrio cholera (open form) — X-ray structure, 2020 (PDB 6U2A), downloaded from the RCSB Protein Data Bank.
S. aureus FtsZ 12-316 F138A GDP Closed form (3FCm) — S. aureus ftsz 12-316 f138a gdp closed form (3fcm) — X-ray structure, 2016 (PDB 5MN6), downloaded from the RCSB Protein Data Bank.
SulA:FtsZ from Pseudomonas aeruginosa — Crystal structure of sula:ftsz from pseudomonas aeruginosa — X-ray structure, 2003 (PDB 1OFU), downloaded from the RCSB Protein Data Bank.
The bacterial cell-division protein zipa and its interaction with an… (1F46) — The bacterial cell-division protein zipa and its interaction with an ftsz fragment revealed by x-ray crystallography — X-ray structure, 2001 (PDB 1F46), downloaded from the RCSB Protein Data Bank.
S. aureus FtsZ 12-316 F138A GDP Open form (1FOf) — S. aureus ftsz 12-316 f138a gdp open form (1fof) — X-ray structure, 2016 (PDB 5MN4), downloaded from the RCSB Protein Data Bank.
GTP-bound, double-stranded, curved FtsZ protofilament structure — Gtp-bound, double-stranded, curved ftsz protofilament structure — X-ray structure, 2018 (PDB 5ZUE), downloaded from the RCSB Protein Data Bank.
Cell-division protein FTSZ at 2.8A resolution — Crystal structure of the cell-division protein ftsz at 2.8a resolution — X-ray structure, 1998 (PDB 1FSZ), downloaded from the RCSB Protein Data Bank.
Staphylococcus aureus FtsZ apo-form — Staphylococcus aureus ftsz apo-form — X-ray structure, 2012 (PDB 3VPA), downloaded from the RCSB Protein Data Bank.
Dimerization of e. coli DNA gyrase b provides a structural mechanism… — Dimerization of e. coli dna gyrase b provides a structural mechanism for activating the atpase catalytic center — X-ray structure, 2000 (PDB 1EI1), downloaded from the RCSB Protein Data Bank.
Putative modulator of DNA gyrase (BT3649) from bacteroides… — Crystal structure of a putative modulator of dna gyrase (bt3649) from bacteroides thetaiotaomicron vpi-5482 at 1.75 a resolution — X-ray structure, 2004 (PDB 1VPB), downloaded from the RCSB Protein Data Bank.
Gyrase b in complex with 4,5-dibromopyrrolamide-based inhibitor — Gyrase b in complex with 4,5-dibromopyrrolamide-based inhibitor — X-ray structure, 2015 (PDB 4ZVI), downloaded from the RCSB Protein Data Bank.
E. coli gyrase b co-complexed with prop-2-yn-1-yl… — Crystal structure of e. coli gyrase b co-complexed with prop-2-yn-1-yl {[5-(4-piperidin-1-yl-2-pyridin-3-yl-1,3-thiazol-5-yl)-1h-pyrazol-3-yl]methyl}carbamate inhibitor — X-ray structure, 2010 (PDB 3G7E), downloaded from the RCSB Protein Data Bank.
A domain insertion in E. coli GyrB adopts a novel fold that plays a… — A domain insertion in e. coli gyrb adopts a novel fold that plays a critical role in gyrase function — X-ray structure, 2010 (PDB 3NUH), downloaded from the RCSB Protein Data Bank.
Dna gyrase B' domain sheds lights on the mechanism for T-segment… — Crystal structure of dna gyrase b' domain sheds lights on the mechanism for t-segment navigation — X-ray structure, 2009 (PDB 2ZJT), downloaded from the RCSB Protein Data Bank.
S. aureus FtsZ 12-316 T66W GTP Closed form (2TCm) — S. aureus ftsz 12-316 t66w gtp closed form (2tcm) — X-ray structure, 2016 (PDB 5MN5), downloaded from the RCSB Protein Data Bank.
Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N… — Structure of streptococcus pneumoniae peptidoglycan deacetylase (sppgda) d 275 n mutant. — X-ray structure, 2005 (PDB 2C1I), downloaded from the RCSB Protein Data Bank.
Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) — Structure of streptococcus pneumoniae peptidoglycan deacetylase (sppgda) — X-ray structure, 2005 (PDB 2C1G), downloaded from the RCSB Protein Data Bank.
Putative modulator of a DNA gyrase (TM0727) from thermotoga maritima… — Crystal structure of a putative modulator of a dna gyrase (tm0727) from thermotoga maritima msb8 at 1.95 a resolution — X-ray structure, 2004 (PDB 1VL4), downloaded from the RCSB Protein Data Bank.
E. coli 24kDa Domain in Complex with Clorobiocin — Crystal structure of e. coli 24kda domain in complex with clorobiocin — X-ray structure, 2002 (PDB 1KZN), downloaded from the RCSB Protein Data Bank.
43K ATPase domain of Thermus thermophilus gyrase B — Crystal structure of the 43k atpase domain of thermus thermophilus gyrase b in complex with novobiocin — X-ray structure, 2002 (PDB 1KIJ), downloaded from the RCSB Protein Data Bank.
The bacterial cell-division protein zipa and its interaction with an… (1F47) — The bacterial cell-division protein zipa and its interaction with an ftsz fragment revealed by x-ray crystallography — X-ray structure, 2001 (PDB 1F47), downloaded from the RCSB Protein Data Bank.