Penicillin-binding protein 3D structures

3D structures of penicillin-binding protein

Updated on 17-September-2020

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• Penicillin-binding protein; Domains - transpeptidase (TP) 234-588
  • 1qme, 1rp5, 2z2l, 5oau – SpPBP 2X – Streptococcus pneumoniae
    
  • 1k25, 1pyy – SpPBP 2X (mutant)
    
  • 5u47 - PBP 2X – Streptococcus thermophilus
    
  • 2fff - SpPBP 1B
    
  • 2bg1, 2xd5 - SpPBP 1B (mutant)
    
  • 2c6w, 2v2f - SpPBP 1A
    
  • 2wad, 2wae, 2waf – SpPBP 2B
    
  • 3vma – EcPBP 1B - Escherichia coli
    
  • 6g5r, 6fzk – EcPBP 1B UB2H domain 108-200 – NMR
    
  • 4bjp – EcPBP 3 residues 67-577
    
  • 6hzq – EcPBP 3 TP domain
    
  • 4bjq – EcPBP 3 residues 88-165
    
  • 2ex2 – EcPBP 4
    
  • 1nzo, 1nzu – EcPBP 5
    
  • 1hd8, 1nj4, 1sdn – EcPBP 5 (mutant)
    
  • 3it9 – EcPBP 6
    
  • 5tro - SaPBP 1 dimerization and TP domains – Staphylococcus aureus
    
  • 1mwr, 1vqq, 4bl2, 4bl3, 4cpk - SaPBP 2A (mutant)
    
  • 2olu, 3dwk, 5m1a, 5m19, 5m18 – SaPBP 2
    
  • 3vsk - SaPBP 3
    
  • 1tvf – SaPBP 4
    
  • 6dz8, 6c3k – SaPBP 4 (mutant)
    
  • 1w5d – BsPBP 4A – Bacillus subtilis
    
  • 3mfd – BsPBP 5*
    
  • 2oqo – AaPBP 1A – Aquifex aeolicus
    
  • 3equ – NgPBP 2 – Neisseria gonorrhoeae
    
  • 3eqv, 5ksh – NgPBP 2 (mutant)
    
  • 6p52, 6p53 – NgPBP 2 TP domain
    
  • 6p56, 4u3t – NgPBP 2 TP domain (mutant)
    
  • 5u2g – HiPBP 1A – Haemophilus influenza
    
  • 6hzo – HiPBP 3 TP domain
    
  • 3a3d – HiPBP 4
    
  • 3a3j – HiPBP 5
    
  • 3lo7, 3un7, 5crf – MtPBP A – Mycobacterium tuberculosis
    
  • 6kgh – MtPBP 3
    
  • 3oc2, 3pbn, 6hr4, 6hzr – PaPBP 3 – Pseudomonas aeruginosa
    
  • 6r40 - PaPBP 3 (mutant)
    
  • 3tg9 – PBP – Bacillus halodurans
    
  • 3udf – AbPBP – Acinetobacter baumannii
    
  • 3zg7 – LmPBP 4 – Listeria monocytogenes
    
  • 5dvy, 5e31 – EfPBP 2 – Enterococcus faecium
    
  • 6bsq - EfPBP 4
    
  • 6g0k - EfPBP 5 (mutant)
    
  • 5lp4 – HpPBP 2 – Helicobacter pylori
    
  • 6hzh – CtPBP 3 TP domain – Chlamydia trachomatis
    
  • 6hzi – PBP 3 TP domain – Burkholderia pseudomallei
    
• Penicillin-binding protein complex with antibiotics
  • 1qmf, 2z2m, 2zc3, 2zc4, 2zc5, 2zc6, 5oj1, 5oj0, 5oiz – SpPBP 2X + antibiotic
    
  • 2c5w - SpPBP 1A + antibiotic
    
  • 2jch, 2je5, 2xd1 - SpPBP 1B (mutant) + antibiotic
    
  • 1mwu, 1mwt, 1mws - SaPBP 2A (mutant) + antibiotic
    
  • 2uwx - SaPBP 1B (mutant) + antibiotic
    
  • 2olv - SaPBP 2 + antibiotic
    
  • 3zfz, 3zg0, 4dki - SaPBP 2’ + antibiotic
    
  • 3vsl - SaPBP 3 + antibiotic
    
  • 5txi, 5ty7, 5tw8 - SaPBP 4 + antibiotic
    
  • 3hum, 3hun, 5ty2, 5tx9, 5tw4 - SaPBP 4 (mutant) + antibiotic
    
  • 6i1i – EcPBP 3 TP domain + antibiotic
    
  • 2ex6, 2ex8, 2ex9, 2exa, 2exb - EcPBP 4 + antibiotic
    
  • 3beb, 3bec, 3mzd, 3mze, 3mzf - EcPBP 5 + antibiotic
    
  • 3ita - EcPBP 6 + antibiotic
    
  • 3fwl, 5hld, 5hlb, 5hla, 5hl9 – EcPBP 1B + antibiotic
    
  • 3a3e, 3a3f, 3a3i – HiPBP 4 + antibiotic
    
  • 4oon – PaPBP 1A + antibiotic
    
  • 3ocl, 3ocn, 3pbo, 3pbq, 3pbr, 3pbs, 3pbt, 4kqo, 4kqq, 4kqr, 4l0l, 6un1, 6hr6, 6i1e, 6r3x, 6un3, 6vje – PaPBP 3 + antibiotic
    
  • 6hr9, 6r42 – PaPBP 3 (mutant) + antibiotic
    
  • 3nb6, 3nb7 - AaPBP 1A + antibiotic
    
  • 3udi, 3udx, 3ue0, 3ue1 - AbPBP + antibiotic
    
  • 3upn, 3upp, 5cxw - MtPBP A + antibiotic
    
  • 3upo - MtPBP A (mutant) + antibiotic
    
  • 6kgs, 6kgt, 6kgu, 6kgv, 6kgw – MtPBP 3 + antibiotic
    
  • 3zg8, 3zg9, 3zga - LmPBP 4 + antibiotic
    
  • 6mkh, 6mki, 6bsr - EfPBP 4 + antibiotic
    
  • 6g88 - EfPBP 5 + antibiotic
    
  • 6p54, 6p55 – NgPBP 2 TP domain + antibiotic
    
  • 6i1f, 6i1g, 6i1h – CtPBP 3 TP domain + antibiotic
    
• Penicillin-binding protein complex with boronic acid derivatives
  • 1z6f – EcPBP 5 + boronic acid
    
  • 2y2g, 2y2h, 2y2i, 2y2j, 2y2k, 2y2l, 2y2m, 2y2n, 2y2o, 2y2p, 2y2q - SpPBP 1B + boronic acid derivative
• Penicillin-binding protein complex with peptidoglycan
  • 3itb - EcPBP 6 + peptidoglycan peptide
    
  • 2j9p - BsPBP 4A + peptidoglycan peptide
    
  • 3zg5 - SaPBP + peptidoglycan analog
    
• Penicillin-binding protein other complexes
  • 4fsf, 4wel, 4wej, 6vot, 6y6u, 6y6z - PaPBP 3 + inhibitor
    
  • 4wek – PaPBP 3 (mutant) + inhibitor
    
  • 5fgz – EcPBP 1B + inhibitor
    
  • 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
    
• PBP D-alanyl-D-alanine carboxypeptidase or DD-transpeptidase
  • 1skf – StDADC - Streptomyces
    
  • 1es2, 1es3, 1es4, 1es5, 1esi, 1j9m – StDADC (mutant)
    
  • 1w79, 1w8q, 1w8y – AcDADC - Actinomadura
    
  • 2wke, 4ben – AcDADC + antibiotic
    
  • 2xk1, 2xln, 2y4a, 2y55, 2y59, 3zvt, 3zvw, 4b4x, 4b4z – AcDADC + boronic acid derivative
    
  • 2vgj, 2vgk, 2xdm – AcDADC + peptidoglycan analog
    
  • 3zcz – AcDADC + inhibitor
    
  • 4rye – MtDADC
    
  • 4ppr – MtDACB1 + antibiotic
    
  • 5fsr – EcDADC
    
  • 5j8x – EcDACA + boronic acid derivative
    
  • 6ntz – EcDADC + antibiotic
    
  • 6osu – DADC – Francisella tularensis
    

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Michal Harel