This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


Penicillin-binding protein 3D structures

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:37, 22 August 2023) (edit) (undo)
 
(One intermediate revision not shown.)
Line 4: Line 4:
{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
-
*'''Penicillin-binding protein'''; Domains - transpeptidase (TP) 234-588
+
*'''Penicillin-binding protein'''; Domains - dimerization 39-233; transpeptidase (TP) 234-588; PASTA 597-713
**[[1qme]], [[1rp5]], [[2z2l]], [[5oau]] – SpPBP 2X – ''Streptococcus pneumoniae''<br />
**[[1qme]], [[1rp5]], [[2z2l]], [[5oau]] – SpPBP 2X – ''Streptococcus pneumoniae''<br />
**[[1k25]], [[1pyy]] – SpPBP 2X (mutant) <br />
**[[1k25]], [[1pyy]] – SpPBP 2X (mutant) <br />
-
**[[5u47]] - PBP 2X – ''Streptococcus thermophilus''<br />
+
**[[2fff]], [[7zuh]] - SpPBP 1B<br />
-
**[[2fff]] - SpPBP 1B<br />
+
**[[2bg1]], [[2xd5]] - SpPBP 1B (mutant) <br />
**[[2bg1]], [[2xd5]] - SpPBP 1B (mutant) <br />
**[[2c6w]], [[2v2f]] - SpPBP 1A <br />
**[[2c6w]], [[2v2f]] - SpPBP 1A <br />
**[[2wad]], [[2wae]], [[2waf]] – SpPBP 2B<br />
**[[2wad]], [[2wae]], [[2waf]] – SpPBP 2B<br />
**[[3vma]] – EcPBP 1B - ''Escherichia coli''<br />
**[[3vma]] – EcPBP 1B - ''Escherichia coli''<br />
 +
**[[7lq6]] – EcPBP 1B – Cryo EM<br />
**[[6g5r]], [[6fzk]] – EcPBP 1B UB2H domain 108-200 – NMR<br />
**[[6g5r]], [[6fzk]] – EcPBP 1B UB2H domain 108-200 – NMR<br />
-
**[[4bjp]] – EcPBP 3 residues 67-577<br />
+
**[[4bjp]], [[7ono]] – EcPBP 3 dimerization+TP domain<br />
**[[6hzq]] – EcPBP 3 TP domain <br />
**[[6hzq]] – EcPBP 3 TP domain <br />
**[[4bjq]] – EcPBP 3 residues 88-165<br />
**[[4bjq]] – EcPBP 3 residues 88-165<br />
Line 21: Line 21:
**[[1nzo]], [[1nzu]] – EcPBP 5<br />
**[[1nzo]], [[1nzu]] – EcPBP 5<br />
**[[1hd8]], [[1nj4]], [[1sdn]] – EcPBP 5 (mutant) <br />
**[[1hd8]], [[1nj4]], [[1sdn]] – EcPBP 5 (mutant) <br />
-
**[[3it9]] – EcPBP 6<br />
+
**[[3it9]], [[5fsr]] – EcPBP 6<br />
-
**[[5tro]] - SaPBP 1 dimerization and TP domains – ''Staphylococcus aureus''<br />
+
**[[7o49]] - SaPBP 1 – ''Staphylococcus aureus''<br />
 +
**[[5tro]] - SaPBP 1 dimerization and TP domains<br />
 +
**[[7o4c]], [[7o61]] - SaPBP 1 PASTA domain<br />
**[[1mwr]], [[1vqq]], [[4bl2]], [[4bl3]], [[4cpk]] - SaPBP 2A (mutant) <br />
**[[1mwr]], [[1vqq]], [[4bl2]], [[4bl3]], [[4cpk]] - SaPBP 2A (mutant) <br />
**[[2olu]], [[3dwk]], [[5m1a]], [[5m19]], [[5m18]] – SaPBP 2<br />
**[[2olu]], [[3dwk]], [[5m1a]], [[5m19]], [[5m18]] – SaPBP 2<br />
**[[3vsk]] - SaPBP 3<br />
**[[3vsk]] - SaPBP 3<br />
-
**[[1tvf]] – SaPBP 4<br />
+
**[[1tvf]], [[6c39]] – SaPBP 4<br />
-
**[[6dz8]], [[6c3k]] – SaPBP 4 (mutant)<br />
+
**[[6dz8]], [[6c3k]], [[7kcv]] – SaPBP 4 (mutant)<br />
-
**[[1w5d]] – BsPBP 4A – ''Bacillus subtilis''<br />
+
**[[7bn9]] – BsPBP 3 – ''Bacillus subtilis''<br />
 +
**[[1w5d]] – BsPBP 4A <br />
**[[3mfd]] – BsPBP 5*<br />
**[[3mfd]] – BsPBP 5*<br />
**[[2oqo]] – AaPBP 1A – ''Aquifex aeolicus''<br />
**[[2oqo]] – AaPBP 1A – ''Aquifex aeolicus''<br />
-
**[[3equ]] – NgPBP 2 – ''Neisseria gonorrhoeae''<br />
+
**[[3equ]] – NgPBP 2 dimerization+TP domain – ''Neisseria gonorrhoeae''<br />
-
**[[3eqv]], [[5ksh]] – NgPBP 2 (mutant) <br />
+
**[[3eqv]], [[5ksh]] – NgPBP 2 dimerization+TP domain (mutant) <br />
**[[6p52]], [[6p53]] – NgPBP 2 TP domain<br />
**[[6p52]], [[6p53]] – NgPBP 2 TP domain<br />
-
**[[6p56]], [[4u3t]] – NgPBP 2 TP domain (mutant)<br />
+
**[[4u3t]], [[6p56]], [[6vbc]], [[6vbl]], [[6vbm]], [[6xqv]], [[6xqx]], [[6xqz]] – NgPBP 2 TP domain (mutant
**[[5u2g]] – HiPBP 1A – ''Haemophilus influenza''<br />
**[[5u2g]] – HiPBP 1A – ''Haemophilus influenza''<br />
**[[6hzo]] – HiPBP 3 TP domain<br />
**[[6hzo]] – HiPBP 3 TP domain<br />
**[[3a3d]] – HiPBP 4 <br />
**[[3a3d]] – HiPBP 4 <br />
**[[3a3j]] – HiPBP 5<br />
**[[3a3j]] – HiPBP 5<br />
-
**[[3lo7]], [[3un7]], [[5crf]] – MtPBP A – ''Mycobacterium tuberculosis''<br />
+
**[[3lo7]], [[3un7]], [[4rye]], [[5crf]] – MtPBP A – ''Mycobacterium tuberculosis''<br />
**[[6kgh]] – MtPBP 3<br />
**[[6kgh]] – MtPBP 3<br />
-
**[[3oc2]], [[3pbn]], [[6hr4]], [[6hzr]] – PaPBP 3 – ''Pseudomonas aeruginosa''<br />
+
**[[3oc2]], [[3pbn]], [[6hr4]], [[6hzr]], [[7onx]], [[7ony]], [[7onz]] – PaPBP 3 – ''Pseudomonas aeruginosa''<br />
**[[6r40]] - PaPBP 3 (mutant)<br />
**[[6r40]] - PaPBP 3 (mutant)<br />
**[[3tg9]] – PBP – ''Bacillus halodurans''<br />
**[[3tg9]] – PBP – ''Bacillus halodurans''<br />
-
**[[3udf]] – AbPBP – ''Acinetobacter baumannii''<br />
+
**[[3udf]] – AbPBP 1A – ''Acinetobacter baumannii''<br />
 +
**[[7zg8]] – AbPBP 2 <br />
**[[3zg7]] – LmPBP 4 – ''Listeria monocytogenes''<br />
**[[3zg7]] – LmPBP 4 – ''Listeria monocytogenes''<br />
**[[5dvy]], [[5e31]] – EfPBP 2 – ''Enterococcus faecium''<br />
**[[5dvy]], [[5e31]] – EfPBP 2 – ''Enterococcus faecium''<br />
**[[6bsq]] - EfPBP 4<br />
**[[6bsq]] - EfPBP 4<br />
-
**[[6g0k]] - EfPBP 5 (mutant)<br />
+
**[[6c84]], [[6mka]], [[6mkj]], [[8f67]] - EfPBP 5 <br />
 +
**[[6g0k]], [[8f3f]], [[8f3j]], [[8f3l]], 8f3m]], [[8f3o]], [[8f3p]], [[8f3q]], [[8f3s]], [[8f3t]], [[8f3u]], [[8f3z]] - EfPBP 5 (mutant)<br />
**[[5lp4]] – HpPBP 2 – ''Helicobacter pylori''<br />
**[[5lp4]] – HpPBP 2 – ''Helicobacter pylori''<br />
-
**[[6hzh]] – CtPBP 3 TP domain – ''Chlamydia trachomatis''<br />
+
**[[7u4h]] – CtPBP 1A – ''Chlamydia trachomatis''<br />
 +
**[[6hzh]] – CtPBP 3 TP domain <br />
**[[6hzi]] – PBP 3 TP domain – ''Burkholderia pseudomallei''<br />
**[[6hzi]] – PBP 3 TP domain – ''Burkholderia pseudomallei''<br />
 +
**[[6tii]] – YpPBP 2 dimerization+TP domains – ''Yersinia pestis''<br />
 +
**[[6tud]] – YpPBP 2 TP domain <br />
 +
**[[6syn]] – YpPBP 3 dimerization+TP domains <br />
 +
**[[1skf]] – StPBP - ''Streptomyces''<br />
 +
**[[1es2]], [[1es3]], [[1es4]], [[1es5]], [[1esi]], [[1j9m]] – StPBP (mutant) <br />
 +
**[[1w79]], [[1w8q]], [[1w8y]] – AcPBP - ''Actinomadura''<br />
 +
**[[6osu]] – PBP – ''Francisella tularensis'' <br />
 +
**[[5u47]] - PBP 2X – ''Streptococcus thermophilus<''br />
 +
**[[7rcx]] – CdPBP 2 – ''Clostridium difficile''<br />
 +
**[[7rd0]] – CdPBP 3 <br />
*Penicillin-binding protein complex with antibiotics
*Penicillin-binding protein complex with antibiotics
Line 58: Line 74:
**[[2c5w]] - SpPBP 1A + antibiotic<br />
**[[2c5w]] - SpPBP 1A + antibiotic<br />
**[[2jch]], [[2je5]], [[2xd1]] - SpPBP 1B (mutant) + antibiotic<br />
**[[2jch]], [[2je5]], [[2xd1]] - SpPBP 1B (mutant) + antibiotic<br />
 +
**[[7o4a]], [[7o4b]] - SaPBP 1 + antibiotic<br />
 +
**[[6h5o]] - SaPBP 2A + antibiotic<br />
 +
**[[6q9n]] - SaPBP 2A + antibiotic + inhibitor<br />
**[[1mwu]], [[1mwt]], [[1mws]] - SaPBP 2A (mutant) + antibiotic<br />
**[[1mwu]], [[1mwt]], [[1mws]] - SaPBP 2A (mutant) + antibiotic<br />
**[[2uwx]] - SaPBP 1B (mutant) + antibiotic<br />
**[[2uwx]] - SaPBP 1B (mutant) + antibiotic<br />
Line 63: Line 82:
**[[3zfz]], [[3zg0]], [[4dki]] - SaPBP 2’ + antibiotic<br />
**[[3zfz]], [[3zg0]], [[4dki]] - SaPBP 2’ + antibiotic<br />
**[[3vsl]] - SaPBP 3 + antibiotic<br />
**[[3vsl]] - SaPBP 3 + antibiotic<br />
-
**[[5txi]], [[5ty7]], [[5tw8]] - SaPBP 4 + antibiotic<br />
+
**[[5txi]], [[5ty7]], [[5tw8]], [[7kcy]] - SaPBP 4 + antibiotic<br />
-
**[[3hum]], [[3hun]], [[5ty2]], [[5tx9]], [[5tw4]] - SaPBP 4 (mutant) + antibiotic<br />
+
**[[3hum]], [[3hun]], [[5ty2]], [[5tx9]], [[5tw4]], [[7kcw]], [[7kcx]] - SaPBP 4 (mutant) + antibiotic<br />
**[[6i1i]] – EcPBP 3 TP domain + antibiotic<br />
**[[6i1i]] – EcPBP 3 TP domain + antibiotic<br />
**[[2ex6]], [[2ex8]], [[2ex9]], [[2exa]], [[2exb]] - EcPBP 4 + antibiotic<br />
**[[2ex6]], [[2ex8]], [[2ex9]], [[2exa]], [[2exb]] - EcPBP 4 + antibiotic<br />
-
**[[3beb]], [[3bec]], [[3mzd]], [[3mze]], [[3mzf]] - EcPBP 5 + antibiotic<br />
+
**[[3beb]], [[3bec]], [[3mzd]], [[3mze]], [[3mzf]], [[6ntz]] - EcPBP 5 + antibiotic<br />
**[[3ita]] - EcPBP 6 + antibiotic<br />
**[[3ita]] - EcPBP 6 + antibiotic<br />
**[[3fwl]], [[5hld]], [[5hlb]], [[5hla]], [[5hl9]] – EcPBP 1B + antibiotic<br />
**[[3fwl]], [[5hld]], [[5hlb]], [[5hla]], [[5hl9]] – EcPBP 1B + antibiotic<br />
**[[3a3e]], [[3a3f]], [[3a3i]] – HiPBP 4 + antibiotic<br />
**[[3a3e]], [[3a3f]], [[3a3i]] – HiPBP 4 + antibiotic<br />
**[[4oon]] – PaPBP 1A + antibiotic<br />
**[[4oon]] – PaPBP 1A + antibiotic<br />
-
**[[3ocl]], [[3ocn]], [[3pbo]], [[3pbq]], [[3pbr]], [[3pbs]], [[3pbt]], [[4kqo]], [[4kqq]], [[4kqr]], [[4l0l]], [[6un1]], [[6hr6]], [[6i1e]], [[6r3x]], [[6un3]], [[6vje]] – PaPBP 3 + antibiotic<br />
+
**[[3ocl]], [[3ocn]], [[3pbo]], [[3pbq]], [[3pbr]], [[3pbs]], [[3pbt]], [[4kqo]], [[4kqq]], [[4kqr]], [[4l0l]], [[6un1]], [[6hr6]], [[6i1e]], [[6r3x]], [[6un3]], [[6vje]], [[7jwl]], [[7lc4]] – PaPBP 3 + antibiotic<br />
**[[6hr9]], [[6r42]] – PaPBP 3 (mutant) + antibiotic<br />
**[[6hr9]], [[6r42]] – PaPBP 3 (mutant) + antibiotic<br />
**[[3nb6]], [[3nb7]] - AaPBP 1A + antibiotic<br />
**[[3nb6]], [[3nb7]] - AaPBP 1A + antibiotic<br />
**[[3udi]], [[3udx]], [[3ue0]], [[3ue1]] - AbPBP + antibiotic<br />
**[[3udi]], [[3udx]], [[3ue0]], [[3ue1]] - AbPBP + antibiotic<br />
-
**[[3upn]], [[3upp]], [[5cxw]] - MtPBP A + antibiotic<br />
+
**[[3upn]], [[3upp]], [[4ppr]], [[5cxw]] - MtPBP A + antibiotic<br />
**[[3upo]] - MtPBP A (mutant) + antibiotic<br />
**[[3upo]] - MtPBP A (mutant) + antibiotic<br />
**[[6kgs]], [[6kgt]], [[6kgu]], [[6kgv]], [[6kgw]] – MtPBP 3 + antibiotic<br />
**[[6kgs]], [[6kgt]], [[6kgu]], [[6kgv]], [[6kgw]] – MtPBP 3 + antibiotic<br />
**[[3zg8]], [[3zg9]], [[3zga]] - LmPBP 4 + antibiotic<br />
**[[3zg8]], [[3zg9]], [[3zga]] - LmPBP 4 + antibiotic<br />
**[[6mkh]], [[6mki]], [[6bsr]] - EfPBP 4 + antibiotic<br />
**[[6mkh]], [[6mki]], [[6bsr]] - EfPBP 4 + antibiotic<br />
-
**[[6g88]] - EfPBP 5 + antibiotic<br />
+
**[[6g88]], [[6mkf]], [6mkg]] - EfPBP 5 + antibiotic<br />
-
**[[6p54]], [[6p55]] – NgPBP 2 TP domain + antibiotic<br />
+
**[[8f3g]], [[8f3h]], [[8f3i]], [[8f3n]], [[8f3r]] - EfPBP 5 (mutant) + antibiotic<br />
 +
**[[6p54]], [[6p55]], [[6vbd]], [[6xqy]] – NgPBP 2 TP domain + antibiotic<br />
**[[6i1f]], [[6i1g]], [[6i1h]] – CtPBP 3 TP domain + antibiotic<br />
**[[6i1f]], [[6i1g]], [[6i1h]] – CtPBP 3 TP domain + antibiotic<br />
 +
**[[6tix]], [[6xv5]] – YpPBP 2 TP domain + antibiotic<br />
 +
**[[2wke]], [[4ben]] – AcPBP + antibiotic <br />
 +
**[[7rcw]], [[7rcy]] – CdPBP 2 + antibiotic <br />
*Penicillin-binding protein complex with boronic acid derivatives
*Penicillin-binding protein complex with boronic acid derivatives
-
**[[1z6f]] – EcPBP 5 + boronic acid<br />
+
**[[1z6f]], [[5fsr]] – EcPBP 5 + boronic acid derivative<br />
-
**[[2y2g]], [[2y2h]], [[2y2i]], [[2y2j]], [[2y2k]], [[2y2l]], [[2y2m]], [[2y2n]], [[2y2o]], [[2y2p]], [[2y2q]] - SpPBP 1B + boronic acid derivative
+
**[[2y2g]], [[2y2h]], [[2y2i]], [[2y2j]], [[2y2k]], [[2y2l]], [[2y2m]], [[2y2n]], [[2y2o]], [[2y2p]], [[2y2q]] - SpPBP 1B + boronic acid derivative<br />
 +
**[[7atm]], [[7ato]], [[7atw]], [[7atx]], [[7au0]], [[7au1]], [[7au8]], [[7au9]], [[7aub]], [[7auh]], [[7kis]], [[7kit]], [[7kiv]], [[7kiw]], [[7ly1]] - PaPBP 3 + boronic acid derivative <br />
 +
**[[2xk1]], [[2xln]], [[2y4a]], [[2y55]], [[2y59]], [[3zvt]], [[3zvw]], [[4b4x]], [[4b4z]] – AcPBP + boronic acid derivative <br />
*Penicillin-binding protein complex with peptidoglycan
*Penicillin-binding protein complex with peptidoglycan
Line 95: Line 120:
**[[2j9p]] - BsPBP 4A + peptidoglycan peptide<br />
**[[2j9p]] - BsPBP 4A + peptidoglycan peptide<br />
**[[3zg5]] - SaPBP + peptidoglycan analog<br />
**[[3zg5]] - SaPBP + peptidoglycan analog<br />
 +
**[[2vgj]], [[2vgk]], [[2xdm]] – AcPBP + peptidoglycan analog <br />
*Penicillin-binding protein other complexes
*Penicillin-binding protein other complexes
Line 101: Line 127:
**[[4wek]] – PaPBP 3 (mutant) + inhibitor<br />
**[[4wek]] – PaPBP 3 (mutant) + inhibitor<br />
**[[5fgz]] – EcPBP 1B + inhibitor<br />
**[[5fgz]] – EcPBP 1B + inhibitor<br />
 +
**[[6yn0]] – EcPBP 1B + FtsN peptide<br />
**[[6g9f]], [[6g9p]], [[6g9s]] – EcPBP 2 + inhibitor<br />
**[[6g9f]], [[6g9p]], [[6g9s]] – EcPBP 2 + inhibitor<br />
 +
**[[7onk]], [[7onn]], [[7onw]] – EcPBP 3 dimerization+TP domain + inhibitor<br />
 +
**[[7ok9]] – SaPBP 1 + pentaglycine<br />
**[[4cjn]] – SaPBP 2A + quinazolinine derivative<br />
**[[4cjn]] – SaPBP 2A + quinazolinine derivative<br />
 +
**[[7zui]], [[7zuj]], [[7zuk]], [[7zul]] – SpPBP 1B + lactone<br />
**[[6g9f]], [[6g9p]], [[6g9s]] – EcPBP 2 + inhibitor<br />
**[[6g9f]], [[6g9p]], [[6g9s]] – EcPBP 2 + inhibitor<br />
**[[5lp5]] – HpPBP 2 + MREC <br />
**[[5lp5]] – HpPBP 2 + MREC <br />
**[[6pl5]], [[6pl6]] - PBP 2 + PGT + peptide – ''Thermus thermophilus''<br />
**[[6pl5]], [[6pl6]] - PBP 2 + PGT + peptide – ''Thermus thermophilus''<br />
-
 
+
**[[3zcz]] – AcPBP + inhibitor <br />
-
*PBP D-alanyl-D-alanine carboxypeptidase or DD-transpeptidase
+
**[[8gpw]] – PBP + ligand – ''Klebsiella pneumoniae'' <br />
-
 
+
-
**[[1skf]] – StDADC - Streptomyces<br />
+
-
**[[1es2]], [[1es3]], [[1es4]], [[1es5]], [[1esi]], [[1j9m]] – StDADC (mutant) <br />
+
-
**[[1w79]], [[1w8q]], [[1w8y]] – AcDADC - Actinomadura<br />
+
-
**[[2wke]], [[4ben]] – AcDADC + antibiotic <br />
+
-
**[[2xk1]], [[2xln]], [[2y4a]], [[2y55]], [[2y59]], [[3zvt]], [[3zvw]], [[4b4x]], [[4b4z]] – AcDADC + boronic acid derivative <br />
+
-
**[[2vgj]], [[2vgk]], [[2xdm]] – AcDADC + peptidoglycan analog <br />
+
-
**[[3zcz]] – AcDADC + inhibitor <br />
+
-
**[[4rye]] – MtDADC <br />
+
-
**[[4ppr]] – MtDACB1 + antibiotic <br />
+
-
**[[5fsr]] – EcDADC <br />
+
-
**[[5j8x]] – EcDACA + boronic acid derivative <br />
+
-
**[[6ntz]] – EcDADC + antibiotic <br />
+
-
**[[6osu]] – DADC – ''Francisella tularensis'' <br />
+
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

3D structures of penicillin-binding protein

Updated on 22-August-2023

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

Retrieved from "http://52.214.119.220/wiki/index.php/Penicillin-binding_protein_3D_structures"
Personal tools