SMTL ID : 4r7u.1

Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 4 residues within 4Å: Chain A: C.85, Q.112, D.144, K.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.144, A:K.148

4 x FFQ: [(1R)-1-hydroxypropyl]phosphonic acid(Non-covalent)

FFQ.2: 6 residues within 4Å: Chain A: T.93, M.94, R.95, G.118, C.119, R.401 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.95, A:G.118, A:R.401, A:R.401 Water bridges: A:A.96, A:R.124 FFQ.6: 6 residues within 4Å: Chain B: T.93, M.94, R.95, G.118, C.119, R.401 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.95, B:G.118, B:R.401, B:R.401 FFQ.9: 6 residues within 4Å: Chain C: T.93, M.94, R.95, G.118, C.119, R.401 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.95, C:G.118, C:R.401, C:R.401 FFQ.13: 6 residues within 4Å: Chain D: T.93, M.94, R.95, C.119, R.124, R.401 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.95, D:R.401, D:R.401

4 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.3: 17 residues within 4Å: Chain A: N.27, W.99, R.124, P.125, V.126, D.127, L.128, H.129, K.164, S.166, V.167, G.168, T.308, D.309, I.331, F.332, R.335 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:N.27, A:W.99 Hydrogen bonds: A:N.27, A:N.27, A:R.124, A:D.127, A:L.128, A:H.129, A:K.164, A:S.166, A:V.167, A:G.168, A:D.309, A:R.335 Water bridges: A:R.95, A:R.124, A:R.124, A:R.124, A:E.192, A:T.308, A:T.308, A:E.333 Salt bridges: A:R.124, A:R.124 UD1.5: 17 residues within 4Å: Chain B: N.27, W.99, R.124, P.125, V.126, D.127, L.128, H.129, K.164, S.166, V.167, G.168, T.308, D.309, I.331, F.332, R.335 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.99 Hydrogen bonds: B:N.27, B:R.124, B:D.127, B:L.128, B:H.129, B:K.164, B:S.166, B:V.167, B:G.168, B:D.309, B:R.335 Water bridges: B:R.95, B:R.95, B:R.124, B:R.124, B:R.124, B:E.192, B:R.236, B:T.308, B:T.308, B:D.309 Salt bridges: B:R.124, B:R.124 UD1.8: 17 residues within 4Å: Chain C: N.27, W.99, R.124, P.125, V.126, D.127, L.128, H.129, K.164, S.166, V.167, G.168, T.308, D.309, I.331, F.332, R.335 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.99, C:L.128 Hydrogen bonds: C:N.27, C:R.124, C:D.127, C:L.128, C:H.129, C:K.164, C:S.166, C:V.167, C:G.168, C:D.309, C:R.335 Water bridges: C:R.95, C:R.124, C:R.124, C:R.124, C:T.308, C:D.309 Salt bridges: C:R.124 UD1.12: 17 residues within 4Å: Chain D: N.27, W.99, R.124, P.125, V.126, D.127, L.128, H.129, K.164, S.166, V.167, G.168, T.308, D.309, I.331, F.332, R.335 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:N.27, D:W.99 Hydrogen bonds: D:N.27, D:R.124, D:D.127, D:L.128, D:H.129, D:K.164, D:S.166, D:V.167, D:G.168, D:D.309, D:R.335 Water bridges: D:K.26, D:R.124, D:R.124, D:R.124, D:R.124, D:E.192, D:E.192, D:E.192, D:R.236, D:D.309 Salt bridges: D:R.124, D:R.124

5 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: N.318, A.321, G.324, G.359, D.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.319, A:A.321, A:G.324, A:D.360 NA.7: 5 residues within 4Å: Chain B: N.318, A.321, G.324, G.359, D.360 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.324, B:D.360 NA.10: 5 residues within 4Å: Chain C: N.318, A.321, G.324, G.359, D.360 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.324, C:G.359, C:D.360 NA.11: 2 residues within 4Å: Chain C: E.333 Chain D: E.333 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.333 NA.14: 6 residues within 4Å: Chain D: N.318, A.321, G.324, C.358, G.359, D.360 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.321, D:A.321, D:G.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin. To be Published

Release Date

2014-09-24

Peptides

UDP-N-acetylglucosamine 1-carboxyvinyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

UDP-N-acetylglucosamine 1-carboxyvinyltransferase