SMTL ID : 6cn1.2 (1 other biounit)

2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x EPU: URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID(Non-covalent)

EPU.1: 22 residues within 4Å: Chain A: K.25, N.26, A.97, I.122, S.124, R.125, P.126, V.127, D.128, L.129, H.130, T.166, V.167, S.168, V.169, T.170, T.310, D.311, I.333, F.334, R.337, L.376 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.97, A:I.122, A:T.170, A:L.376 Hydrogen bonds: A:N.26, A:N.26, A:S.124, A:D.128, A:D.128, A:L.129, A:H.130, A:V.167, A:V.169, A:T.170, A:T.170, A:D.311, A:R.337 Salt bridges: A:K.25, A:R.125, A:R.125 EPU.4: 22 residues within 4Å: Chain B: K.25, N.26, A.97, I.122, S.124, R.125, P.126, V.127, D.128, L.129, H.130, T.166, V.167, S.168, V.169, T.170, T.310, D.311, I.333, F.334, R.337, L.376 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.97, B:I.122, B:T.170 Hydrogen bonds: B:N.26, B:N.26, B:S.124, B:D.128, B:L.129, B:V.167, B:V.169, B:T.170, B:D.311, B:R.337 Water bridges: B:R.125, B:R.125, B:T.310, B:T.310 Salt bridges: B:K.25, B:R.125, B:R.125, B:R.125 EPU.8: 21 residues within 4Å: Chain C: K.25, N.26, A.97, S.124, R.125, P.126, V.127, D.128, L.129, H.130, T.166, V.167, S.168, V.169, T.170, T.310, D.311, I.333, F.334, R.337, L.376 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:A.97, C:T.170 Hydrogen bonds: C:N.26, C:N.26, C:S.124, C:D.128, C:L.129, C:V.167, C:V.169, C:T.170, C:D.311, C:R.337 Water bridges: C:R.125, C:T.310, C:R.403 Salt bridges: C:K.25, C:R.125, C:R.125, C:R.125 EPU.11: 21 residues within 4Å: Chain D: K.25, N.26, A.97, S.124, R.125, P.126, V.127, D.128, L.129, H.130, T.166, V.167, S.168, V.169, T.170, T.310, D.311, I.333, F.334, R.337, L.376 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:A.97, D:T.170 Hydrogen bonds: D:N.26, D:N.26, D:S.124, D:D.128, D:D.128, D:L.129, D:V.167, D:V.169, D:T.170, D:T.170, D:T.170, D:D.311, D:R.337 Water bridges: D:R.125, D:R.125 Salt bridges: D:K.25, D:R.125

4 x 0V5: (2R)-2-(phosphonooxy)propanoic acid(Covalent)

0V5.2: 7 residues within 4Å: Chain A: T.94, M.95, R.96, C.120, A.121, R.403 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.96, A:A.121 Water bridges: A:K.93, A:T.94, A:R.403, A:R.403 Salt bridges: A:R.403 0V5.5: 8 residues within 4Å: Chain B: T.94, R.96, C.120, A.121, R.125, L.376, R.403 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.376 Hydrogen bonds: B:R.96, B:A.121, B:R.125 Water bridges: B:R.403, B:R.403 Salt bridges: B:R.403 0V5.9: 9 residues within 4Å: Chain C: T.94, M.95, R.96, G.119, C.120, A.121, I.122, R.403 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.122 Hydrogen bonds: C:R.96, C:A.121 Water bridges: C:A.97, C:R.403, C:R.403, C:R.403 Salt bridges: C:R.403 0V5.12: 10 residues within 4Å: Chain D: T.94, M.95, R.96, G.119, C.120, A.121, R.125, L.376, R.403 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.376 Hydrogen bonds: D:R.96, D:A.121, D:R.125 Water bridges: D:T.94, D:R.403, D:R.403 Salt bridges: D:R.403

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.94, R.403 Ligands: 0V5.2 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.1, H2O.2, H2O.2, 0V5.2 MG.6: 3 residues within 4Å: Chain B: T.94, R.403 Ligands: 0V5.5 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.2, H2O.2, H2O.3, H2O.3, 0V5.5 MG.10: 2 residues within 4Å: Chain C: R.403 Ligands: 0V5.9 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.3, H2O.3, H2O.3, H2O.3, 0V5.9 MG.13: 2 residues within 4Å: Chain D: R.403 Ligands: 0V5.12 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.4, H2O.4, H2O.4, H2O.5, 0V5.12

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain B: Q.413, R.420, R.421 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: P.41, R.80 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: E.266, P.306 Chain D: Q.189 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium. To Be Published

Release Date

2018-03-21

Peptides

UDP-N-acetylglucosamine 1-carboxyvinyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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