Penicillin-binding protein 3D structures

3D structures of penicillin-binding protein

Updated on 21-April-2026

{"openlevels":0}

• Penicillin-binding protein 1; Domains - dimerization 39-233; transpeptidase (TP) 234-588; PASTA 597-713
  • 2c6w, 2v2f - SpPBP 1A - Streptococcus pneumoniae
    
  • 2fff, 7zuh - SpPBP 1B
    
  • 2bg1, 2xd5 - SpPBP 1B (mutant)
    
  • 3vma – EcPBP 1B - Escherichia coli
    
  • 7lq6 – EcPBP 1B – Cryo EM
    
  • 6g5r, 6fzk – EcPBP 1B UB2H domain 108-200 – NMR
    
  • 7o49, 8vbt, 8vbu, 8vbv, 8vbw - SaPBP 1 – Staphylococcus aureus
    
  • 5tro - SaPBP 1 dimerization and TP domains
    
  • 7o4c, 7o61 - SaPBP 1 PASTA domain
    
  • 2oqo – AaPBP 1A – Aquifex aeolicus
    
  • 5u2g – HiPBP 1A – Haemophilus influenza
    
  • 3lo7, 3un7, 4rye, 5crf – MtPBP A – Mycobacterium tuberculosis
    
  • 3tg9 – PBP – Bacillus halodurans
    
  • 3udf – AbPBP 1A – Acinetobacter baumannii
    
  • 7u4h – CtPBP 1A – Chlamydia trachomatis
    
  • 1skf – StPBP - Streptomyces
    
  • 1es2, 1es3, 1es4, 1es5, 1esi, 1j9m – StPBP (mutant)
    
  • 1w79, 1w8q, 1w8y – AcPBP - Actinomadura
    
  • 6osu – PBP – Francisella tularensis
    
• Penicillin-binding protein 2
  • 1pmd, 1qme, 1rp5, 2z2l, 5oau – SpPBP 2X
    
  • 1k25, 1pyy – SpPBP 2X (mutant)
    
  • 2wad, 2wae, 2waf – SpPBP 2B
    
  • 1mwr, 1vqq, 4bl2, 4bl3, 4cpk - SaPBP 2A (mutant)
    
  • 2olu, 3dwk, 5m1a, 5m19, 5m18 – SaPBP 2
    
  • 3equ – NgPBP 2 dimerization+TP domain – Neisseria gonorrhoeae
    
  • 3eqv, 5ksh – NgPBP 2 dimerization+TP domain (mutant)
    
  • 6p52, 6p53 – NgPBP 2 TP domain
    
  • 4u3t, 6p56, 6vbc, 6vbl, 6vbm, 6xqv, 6xqx, 6xqz, 8vbz, 8ven, 8vp, 8veq, 9z0w, 9z0x, 9z0y, 9z5t – NgPBP 2 TP domain (mutant)
  • 7zg8, 8zpc – AbPBP 2
    
  • 5dvy, 5e31 – EfPBP 2 – Enterococcus faecium
    
  • 5lp4 – HpPBP 2 – Helicobacter pylori
    
  • 6tii – YpPBP 2 dimerization+TP domains – Yersinia pestis
    
  • 6tud – YpPBP 2 TP domain
    
  • 5u47 - PBP 2X – Streptococcus thermophilus<br />
  • 7rcx – CdPBP 2 – Clostridium difficile
    
  • 8yjx – PBP 2 – Campylobacter jejuni
    
• Penicillin-binding protein 3
  • 4bjp, 7ono – EcPBP 3 dimerization+TP domain
    
  • 6hzq – EcPBP 3 TP domain
    
  • 4bjq – EcPBP 3 residues 88-165
    
  • 3vsk - SaPBP 3
    
  • 7bn9 – BsPBP 3 – Bacillus subtilis
    
  • 6hzo – HiPBP 3 TP domain
    
  • 6kgh – MtPBP 3
    
  • 3oc2, 3pbn, 6hr4, 6hzr, 7onx, 7ony, 7onz, 9fz8 – PaPBP 3 – Pseudomonas aeruginosa
    
  • 6r40 - PaPBP 3 (mutant)
    
  • 6hzh – CtPBP 3 TP domain
    
  • 6hzi – PBP 3 TP domain – Burkholderia pseudomallei
    
  • 6syn – YpPBP 3 dimerization+TP domains
    
  • 7rd0 – CdPBP 3
    
  • 8c5b – SePBP 3 – Staphylococcus epidermidis
    
• Penicillin-binding protein 4
  • 2ex2 – EcPBP 4
    
  • 1tvf, 6c39 – SaPBP 4
    
  • 6dz8, 6c3k, 7kcv – SaPBP 4 (mutant)
    
  • 1w5d – BsPBP 4A
    
  • 3a3d – HiPBP 4
    
  • 3zg7, 5zqa – LmPBP 4 – Listeria monocytogenes
    
  • 6bsq - EfPBP 4
    
• Penicillin-binding protein 5
  • 1nzo, 1nzu – EcPBP 5
    
  • 1hd8, 1nj4, 1sdn – EcPBP 5 (mutant)
    
  • 3mfd – BsPBP 5*
    
  • 3a3j – HiPBP 5
    
  • 6c84, 6mka, 6mkj, 8f67, 8u55 - EfPBP 5
    
  • 6g0k, 8f3f, 8f3j, 8f3l, 8f3m, 8f3o, 8f3p, 8f3q, 8f3s, 8f3t, 8f3u, 8f3v, 8f3w, 8f3x, 8f3y, 8f3z, 9d25 - EfPBP 5 (mutant)
    
  • 4k91 – PaPBP 5
    
• Penicillin-binding protein 6
  • 3it9, 5fsr – EcPBP 6
    
• Penicillin-binding protein 1 complex with antibiotics
  • 2c5w - SpPBP 1A + antibiotic
    
  • 2jch, 2je5, 2xd1, 9ssd, 9sse, 9ssf, 9ssg, 9ssh, 9ssi - SpPBP 1B (mutant) + antibiotic
    
  • 7o4a, 7o4b - SaPBP 1 + antibiotic
    
  • 2uwx - SaPBP 1B (mutant) + antibiotic
    
  • 3fwl, 5hld, 5hlb, 5hla, 5hl9 – EcPBP 1B + antibiotic
    
  • 4oon, 5df7, 5df8, 5df9 – PaPBP 1A + antibiotic
    
  • 3nb6, 3nb7 - AaPBP 1A + antibiotic
    
  • 3udi, 3udx, 3ue0, 3ue1 - AbPBP + antibiotic
    
  • 3upn, 3upp, 4ppr, 5cxw - MtPBP A + antibiotic
    
  • 3upo - MtPBP A (mutant) + antibiotic
    
  • 2wke, 4ben – AcPBP + antibiotic
    
• Penicillin-binding protein 2 complex with antibiotics
  • 6h5o - SaPBP 2A + antibiotic
    
  • 6q9n - SaPBP 2A + antibiotic + inhibitor
    
  • 1mwu, 1mwt, 1mws - SaPBP 2A (mutant) + antibiotic
    
  • 2olv - SaPBP 2 + antibiotic
    
  • 3zfz, 3zg0, 4dki - SaPBP 2’ + antibiotic
    
  • 6p54, 6p55, 6vbd, 6xqy – NgPBP 2 TP domain + antibiotic
    
  • 6tix, 6xv5 – YpPBP 2 TP domain + antibiotic
    
  • 7rcw, 7rcy – CdPBP 2 + antibiotic
    
  • 1qmf, 2z2m, 2zc3, 2zc4, 2zc5, 2zc6, 5oj1, 5oj0, 5oiz – SpPBP 2X + antibiotic
    
• Penicillin-binding protein 3 complex with antibiotics
  • 3vsl - SaPBP 3 + antibiotic
    
  • 6i1i – EcPBP 3 TP domain + antibiotic
    
  • 3ocl, 3ocn, 3pbo, 3pbq, 3pbr, 3pbs, 3pbt, 4kqo, 4kqq, 4kqr, 4l0l, 6un1, 6hr6, 6i1e, 6r3x, 6un3, 6vje, 7jwl, 7lc4, 9fz7, 9fze, 9fzo, 9fzp – PaPBP 3 + antibiotic
    
  • 6hr9, 6r42 – PaPBP 3 (mutant) + antibiotic
    
  • 6kgs, 6kgt, 6kgu, 6kgv, 6kgw – MtPBP 3 + antibiotic
    
  • 6i1f, 6i1g, 6i1h – CtPBP 3 TP domain + antibiotic
    
  • 8c5o, 8c5w – SePBP 3 + antibiotic
    
• Penicillin-binding protein 4 complex with antibiotics
  • 5txi, 5ty7, 5tw8, 7kcy - SaPBP 4 + antibiotic
    
  • 3hum, 3hun, 5ty2, 5tx9, 5tw4, 7kcw, 7kcx - SaPBP 4 (mutant) + antibiotic
    
  • 2ex6, 2ex8, 2ex9, 2exa, 2exb - EcPBP 4 + antibiotic
    
  • 3a3e, 3a3f, 3a3i – HiPBP 4 + antibiotic
    
  • 3zg8, 3zg9, 3zga, 5zqb, 5zqc, 5zqd, 5zqf - LmPBP 4 + antibiotic
    
  • 6mkh, 6mki, 6bsr - EfPBP 4 + antibiotic
    
• Penicillin-binding protein 5 complex with antibiotics
  • 3beb, 3bec, 3mzd, 3mze, 3mzf, 6ntz - EcPBP 5 + antibiotic
    
  • 6g88, 6mkf, 6mkg - EfPBP 5 + antibiotic
    
  • 8f3g, 8f3h, 8f3i, 8f3n, 8f3r - EfPBP 5 (mutant) + antibiotic
    
• Penicillin-binding protein 6 complex with antibiotics
  • 3ita - EcPBP 6 + antibiotic
    
• Penicillin-binding protein complex with boronic acid derivatives
  • 2y2g, 2y2h, 2y2i, 2y2j, 2y2k, 2y2l, 2y2m, 2y2n, 2y2o, 2y2p, 2y2q - SpPBP 1B + boronic acid derivative
    
  • 2xk1, 2xln, 2y4a, 2y55, 2y59, 3zvt, 3zvw, 4b4x, 4b4z – AcPBP + boronic acid derivative
    
  • 9mcz, 9md0 – NgPBP 2 TP domain + boronic acid derivative
    
  • 7atm, 7ato, 7atw, 7atx, 7au0, 7au1, 7au8, 7au9, 7aub, 7auh, 7kis, 7kit, 7kiv, 7kiw, 7ly1 - PaPBP 3 + boronic acid derivative
    
  • 1z6f, 5fsr – EcPBP 5 + boronic acid derivative
    
• Penicillin-binding protein complex with peptidoglycan
  • 3itb - EcPBP 6 + peptidoglycan peptide
    
  • 2j9p - BsPBP 4A + peptidoglycan peptide
    
  • 3zg5 - SaPBP + peptidoglycan analog
    
  • 2vgj, 2vgk, 2xdm – AcPBP + peptidoglycan analog
    
• Penicillin-binding protein other complexes
  • 9sg5, 9sg6, 9sg7, 9sg8, 9sg9, 9sga, 9sgb, 9sgc, 9sgd, 9sge – SpPBP 1B + monobactam
    
  • 7zui, 7zuj, 7zuk, 7zul – SpPBP 1B + lactone
    
  • 5fgz – EcPBP 1B + inhibitor
    
  • 6yn0 – EcPBP 1B + FtsN peptide
    
  • 7ok9 – SaPBP 1 + pentaglycine
    
  • 3zcz – AcPBP + inhibitor
    
  • 8gpw – PBP + ligand – Klebsiella pneumoniae
    
  • 6g9f, 6g9p, 6g9s – EcPBP 2 + inhibitor
    
  • 4cjn – SaPBP 2A + quinazolinine derivative
    
  • 6g9f, 6g9p, 6g9s – EcPBP 2 + inhibitor
    
  • 5lp5 – HpPBP 2 + MREC
    
  • 6pl5, 6pl6 - PBP 2 + PGT + peptide – Thermus thermophilus
    
  • 7onk, 7onn, 7onw – EcPBP 3 dimerization+TP domain + inhibitor
    
  • 8rtz – EcPBP 3 + peptide inhibitor
    
  • 4fsf, 4wel, 4wej, 6vot, 6y6u, 6y6z - PaPBP 3 + inhibitor
    
  • 4wek – PaPBP 3 (mutant) + inhibitor
    

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel