SMTL ID : 1j2z.2 (1 other biounit)

Crystal structure of UDP-N-acetylglucosamine acyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x SOG: octyl 1-thio-beta-D-glucopyranoside(Non-covalent)

SOG.1: 14 residues within 4Å: Chain A: Q.69, D.70, H.118, A.120, H.121, L.137, A.138, G.139, H.156, Q.157, R.253 Chain C: N.133 Chain E: Y.257, S.260 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.138, A:Q.157, A:Q.157 Hydrogen bonds: A:Q.69, A:D.70, A:H.121, A:G.139, C:N.133 Water bridges: A:N.95, A:H.121, C:N.133 SOG.5: 14 residues within 4Å: Chain A: N.133 Chain B: Q.69, D.70, H.118, A.120, H.121, L.137, A.138, G.139, H.156, Q.157, R.253 Chain D: Y.257, S.260 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.138, B:Q.157, B:Q.157 Hydrogen bonds: B:Q.69, B:D.70, B:H.121, B:G.139, A:N.133 Water bridges: B:N.95, B:H.121, A:N.133 SOG.9: 14 residues within 4Å: Chain B: N.133 Chain C: Q.69, D.70, H.118, A.120, H.121, L.137, A.138, G.139, H.156, Q.157, R.253 Chain F: Y.257, S.260 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.138, C:Q.157, C:Q.157 Hydrogen bonds: C:Q.69, C:D.70, C:H.121, C:G.139, B:N.133 Water bridges: C:N.95, C:H.121, B:N.133 SOG.13: 14 residues within 4Å: Chain B: Y.257, S.260 Chain D: Q.69, D.70, H.118, A.120, H.121, L.137, A.138, G.139, H.156, Q.157, R.253 Chain F: N.133 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:A.138, D:Q.157, D:Q.157 Hydrogen bonds: D:Q.69, D:D.70, D:D.70, D:H.118, D:G.139, F:N.133 Water bridges: D:N.95, D:H.121, F:N.133 SOG.17: 14 residues within 4Å: Chain A: Y.257, S.260 Chain D: N.133 Chain E: Q.69, D.70, H.118, A.120, H.121, L.137, A.138, G.139, H.156, Q.157, R.253 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:A.138, E:Q.157, E:Q.157 Hydrogen bonds: E:Q.69, E:D.70, E:D.70, E:H.118, E:G.139, D:N.133 Water bridges: E:N.95, E:H.121, D:N.133 SOG.21: 14 residues within 4Å: Chain C: Y.257, S.260 Chain E: N.133 Chain F: Q.69, D.70, H.118, A.120, H.121, L.137, A.138, G.139, H.156, Q.157, R.253 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:A.138, F:Q.157, F:Q.157 Hydrogen bonds: F:Q.69, F:D.70, F:D.70, F:H.118, F:G.139, E:N.133 Water bridges: F:N.95, F:H.121, E:N.133

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: Q.47, T.66, Q.67 Chain C: H.41, F.59 Ligands: TLA.4 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:Q.47, A:Q.67, A:Q.67 Water bridges: A:G.65, C:K.39, C:K.39, C:K.39, C:H.41 Salt bridges: C:H.41 SO4.3: 5 residues within 4Å: Chain A: K.3, I.4, A.5, K.6, E.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.6, A:E.24 Salt bridges: A:K.3 SO4.6: 6 residues within 4Å: Chain A: H.41, F.59 Chain B: Q.47, T.66, Q.67 Ligands: TLA.8 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:K.39, A:K.39, A:K.39, A:H.41, B:G.65 Salt bridges: A:H.41 Hydrogen bonds: B:Q.47, B:Q.67, B:Q.67 SO4.7: 5 residues within 4Å: Chain B: K.3, I.4, A.5, K.6, E.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.6, B:E.24 Salt bridges: B:K.3 SO4.10: 6 residues within 4Å: Chain B: H.41, F.59 Chain C: Q.47, T.66, Q.67 Ligands: TLA.12 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Water bridges: B:K.39, B:K.39, B:K.39, B:H.41, C:G.65 Salt bridges: B:H.41 Hydrogen bonds: C:Q.47, C:Q.67, C:Q.67 SO4.11: 5 residues within 4Å: Chain C: K.3, I.4, A.5, K.6, E.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.6, C:E.24 Salt bridges: C:K.3 SO4.14: 6 residues within 4Å: Chain D: Q.47, T.66, Q.67 Chain F: H.41, F.59 Ligands: TLA.16 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain D Water bridges: F:K.39, F:K.39, F:K.39, D:G.65 Salt bridges: F:H.41 Hydrogen bonds: D:Q.47, D:Q.67, D:Q.67 SO4.15: 5 residues within 4Å: Chain D: K.3, I.4, A.5, K.6, E.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.6, D:E.24 Salt bridges: D:K.3 SO4.18: 6 residues within 4Å: Chain D: H.41, F.59 Chain E: Q.47, T.66, Q.67 Ligands: TLA.20 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:Q.47, E:Q.67, E:Q.67 Water bridges: E:G.65, D:K.39, D:K.39, D:K.39 Salt bridges: D:H.41 SO4.19: 5 residues within 4Å: Chain E: K.3, I.4, A.5, K.6, E.24 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.6, E:E.24 Salt bridges: E:K.3 SO4.22: 6 residues within 4Å: Chain E: H.41, F.59 Chain F: Q.47, T.66, Q.67 Ligands: TLA.24 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:Q.47, F:Q.67, F:Q.67 Water bridges: F:G.65, E:K.39, E:K.39, E:K.39 Salt bridges: E:H.41 SO4.23: 5 residues within 4Å: Chain F: K.3, I.4, A.5, K.6, E.24 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.6, F:E.24 Salt bridges: F:K.3

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 5 residues within 4Å: Chain A: G.29, D.30, Q.47, G.48 Ligands: SO4.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.30, A:D.30, A:Q.47, A:G.48 Water bridges: A:D.30, A:D.30, A:D.30, A:G.31, A:Q.47 TLA.8: 5 residues within 4Å: Chain B: G.29, D.30, Q.47, G.48 Ligands: SO4.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.30, B:D.30, B:Q.47, B:G.48 Water bridges: B:D.30, B:D.30, B:D.30, B:G.31, B:Q.47 TLA.12: 5 residues within 4Å: Chain C: G.29, D.30, Q.47, G.48 Ligands: SO4.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.30, C:D.30, C:Q.47, C:G.48 Water bridges: C:D.30, C:D.30, C:D.30, C:G.31, C:Q.47 TLA.16: 5 residues within 4Å: Chain D: G.29, D.30, Q.47, G.48 Ligands: SO4.14 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.30, D:D.30, D:Q.47, D:G.48 Water bridges: D:D.30, D:D.30, D:D.30, D:D.30, D:Q.47 TLA.20: 5 residues within 4Å: Chain E: G.29, D.30, Q.47, G.48 Ligands: SO4.18 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:D.30, E:D.30, E:Q.47, E:G.48 Water bridges: E:D.30, E:D.30, E:D.30, E:D.30, E:Q.47 TLA.24: 5 residues within 4Å: Chain F: G.29, D.30, Q.47, G.48 Ligands: SO4.22 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:D.30, F:D.30, F:Q.47, F:G.48 Water bridges: F:D.30, F:D.30, F:D.30, F:D.30, F:Q.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.I. et al., Crystal structure of UDP-N-acetylglucosamine acyltransferase from Helicobacter pylori. Proteins (2003)

Release Date

2004-01-27

Peptides

Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase

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