Penicillin-binding protein 3D structures

From Proteopedia

3D structures of penicillin-binding protein

Updated on 22-August-2023

Penicillin-binding protein; Domains - dimerization 39-233; transpeptidase (TP) 234-588; PASTA 597-713

1qme, 1rp5, 2z2l, 5oau – SpPBP 2X – Streptococcus pneumoniae

1k25, 1pyy – SpPBP 2X (mutant)

2fff, 7zuh - SpPBP 1B

2bg1, 2xd5 - SpPBP 1B (mutant)

2c6w, 2v2f - SpPBP 1A

2wad, 2wae, 2waf – SpPBP 2B

3vma – EcPBP 1B - Escherichia coli

7lq6 – EcPBP 1B – Cryo EM

6g5r, 6fzk – EcPBP 1B UB2H domain 108-200 – NMR

4bjp, 7ono – EcPBP 3 dimerization+TP domain

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, 5fsr – EcPBP 6

7o49 - SaPBP 1 – Staphylococcus aureus

5tro - SaPBP 1 dimerization and TP domains

7o4c, 7o61 - SaPBP 1 PASTA domain

1mwr, 1vqq, 4bl2, 4bl3, 4cpk - SaPBP 2A (mutant)

2olu, 3dwk, 5m1a, 5m19, 5m18 – SaPBP 2

3vsk - SaPBP 3

1tvf, 6c39 – SaPBP 4

6dz8, 6c3k, 7kcv – SaPBP 4 (mutant)

7bn9 – BsPBP 3 – Bacillus subtilis

1w5d – BsPBP 4A

3mfd – BsPBP 5*

2oqo – AaPBP 1A – Aquifex aeolicus

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 – NgPBP 2 TP domain (mutant

5u2g – HiPBP 1A – Haemophilus influenza

6hzo – HiPBP 3 TP domain

3a3d – HiPBP 4

3a3j – HiPBP 5

3lo7, 3un7, 4rye, 5crf – MtPBP A – Mycobacterium tuberculosis

6kgh – MtPBP 3

3oc2, 3pbn, 6hr4, 6hzr, 7onx, 7ony, 7onz – PaPBP 3 – Pseudomonas aeruginosa

6r40 - PaPBP 3 (mutant)

3tg9 – PBP – Bacillus halodurans

3udf – AbPBP 1A – Acinetobacter baumannii

7zg8 – AbPBP 2

3zg7 – LmPBP 4 – Listeria monocytogenes

5dvy, 5e31 – EfPBP 2 – Enterococcus faecium

6bsq - EfPBP 4

6c84, 6mka, 6mkj, 8f67 - EfPBP 5

6g0k, 8f3f, 8f3j, 8f3l, 8f3m]], 8f3o, 8f3p, 8f3q, 8f3s, 8f3t, 8f3u, 8f3z - EfPBP 5 (mutant)

5lp4 – HpPBP 2 – Helicobacter pylori

7u4h – CtPBP 1A – Chlamydia trachomatis

6hzh – CtPBP 3 TP domain

6hzi – PBP 3 TP domain – Burkholderia pseudomallei

6tii – YpPBP 2 dimerization+TP domains – Yersinia pestis

6tud – YpPBP 2 TP domain

6syn – YpPBP 3 dimerization+TP domains

1skf – StPBP - Streptomyces

1es2, 1es3, 1es4, 1es5, 1esi, 1j9m – StPBP (mutant)

1w79, 1w8q, 1w8y – AcPBP - Actinomadura

6osu – PBP – Francisella tularensis

5u47 - PBP 2X – Streptococcus thermophilus<br />

7rcx – CdPBP 2 – Clostridium difficile

7rd0 – CdPBP 3

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

7o4a, 7o4b - SaPBP 1 + antibiotic

6h5o - SaPBP 2A + antibiotic

6q9n - SaPBP 2A + antibiotic + inhibitor

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, 7kcy - SaPBP 4 + antibiotic

3hum, 3hun, 5ty2, 5tx9, 5tw4, 7kcw, 7kcx - SaPBP 4 (mutant) + antibiotic

6i1i – EcPBP 3 TP domain + antibiotic

2ex6, 2ex8, 2ex9, 2exa, 2exb - EcPBP 4 + antibiotic

3beb, 3bec, 3mzd, 3mze, 3mzf, 6ntz - 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, 7jwl, 7lc4 – PaPBP 3 + antibiotic

6hr9, 6r42 – PaPBP 3 (mutant) + antibiotic

3nb6, 3nb7 - AaPBP 1A + antibiotic

3udi, 3udx, 3ue0, 3ue1 - AbPBP + antibiotic

3upn, 3upp, 4ppr, 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, 6mkf, [6mkg]] - EfPBP 5 + antibiotic

8f3g, 8f3h, 8f3i, 8f3n, 8f3r - EfPBP 5 (mutant) + antibiotic

6p54, 6p55, 6vbd, 6xqy – NgPBP 2 TP domain + antibiotic

6i1f, 6i1g, 6i1h – CtPBP 3 TP domain + antibiotic

6tix, 6xv5 – YpPBP 2 TP domain + antibiotic

2wke, 4ben – AcPBP + antibiotic

7rcw, 7rcy – CdPBP 2 + antibiotic

Penicillin-binding protein complex with boronic acid derivatives

1z6f, 5fsr – EcPBP 5 + boronic acid derivative

2y2g, 2y2h, 2y2i, 2y2j, 2y2k, 2y2l, 2y2m, 2y2n, 2y2o, 2y2p, 2y2q - SpPBP 1B + boronic acid derivative

7atm, 7ato, 7atw, 7atx, 7au0, 7au1, 7au8, 7au9, 7aub, 7auh, 7kis, 7kit, 7kiv, 7kiw, 7ly1 - PaPBP 3 + boronic acid derivative

2xk1, 2xln, 2y4a, 2y55, 2y59, 3zvt, 3zvw, 4b4x, 4b4z – AcPBP + 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

4fsf, 4wel, 4wej, 6vot, 6y6u, 6y6z - PaPBP 3 + inhibitor

4wek – PaPBP 3 (mutant) + inhibitor

5fgz – EcPBP 1B + inhibitor

6yn0 – EcPBP 1B + FtsN peptide

6g9f, 6g9p, 6g9s – EcPBP 2 + inhibitor

7onk, 7onn, 7onw – EcPBP 3 dimerization+TP domain + inhibitor

7ok9 – SaPBP 1 + pentaglycine

4cjn – SaPBP 2A + quinazolinine derivative

7zui, 7zuj, 7zuk, 7zul – SpPBP 1B + lactone

6g9f, 6g9p, 6g9s – EcPBP 2 + inhibitor

5lp5 – HpPBP 2 + MREC

6pl5, 6pl6 - PBP 2 + PGT + peptide – Thermus thermophilus

3zcz – AcPBP + inhibitor

8gpw – PBP + ligand – Klebsiella pneumoniae