SMTL ID : 2gn4.1

Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADPH and UDP-GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 29 residues within 4Å: Chain A: G.28, T.30, G.31, S.32, F.33, S.54, R.55, D.56, K.59, G.77, D.78, V.79, A.98, A.99, A.100, K.102, T.117, L.140, S.141, T.142, Y.152, K.156, Y.182, G.183, N.184, V.185, S.188, R.189 Ligands: UD1.2 35 PLIP interactions: 34 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.182, A:V.185 Hydrogen bonds: A:G.28, A:T.30, A:T.30, A:S.32, A:F.33, A:R.55, A:R.55, A:D.56, A:D.78, A:V.79, A:A.98, A:A.100, A:K.102, A:Y.152, A:K.156, A:V.185, A:S.188, A:S.188, A:S.188 Water bridges: A:G.31, A:G.34, A:S.54, A:K.59, A:K.59, A:R.80, A:R.189, B:D.56 Salt bridges: A:R.55, A:K.59, A:K.102, A:K.102, A:R.189 pi-Cation interactions: A:R.55 NDP.3: 29 residues within 4Å: Chain B: G.28, T.30, G.31, S.32, F.33, S.54, R.55, D.56, K.59, G.77, D.78, V.79, A.98, A.99, A.100, K.102, T.117, L.140, S.141, T.142, Y.152, K.156, Y.182, G.183, N.184, V.185, S.188, R.189 Ligands: UD1.4 35 PLIP interactions: 33 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.182, B:V.185 Hydrogen bonds: B:G.28, B:T.30, B:T.30, B:S.32, B:F.33, B:R.55, B:R.55, B:D.56, B:D.78, B:V.79, B:A.98, B:A.100, B:K.102, B:K.156, B:V.185, B:S.188, B:S.188, B:S.188 Water bridges: B:G.31, B:G.34, B:S.54, B:K.59, B:K.59, B:R.80, B:S.188, A:D.56, A:E.57 Salt bridges: B:R.55, B:K.59, B:K.102, B:K.102, B:R.189 pi-Cation interactions: B:R.55 NDP.7: 29 residues within 4Å: Chain C: G.28, T.30, G.31, S.32, F.33, S.54, R.55, D.56, K.59, G.77, D.78, V.79, A.98, A.99, A.100, K.102, T.117, L.140, S.141, T.142, Y.152, K.156, Y.182, G.183, N.184, V.185, S.188, R.189 Ligands: UD1.8 35 PLIP interactions: 34 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.182, C:V.185 Hydrogen bonds: C:G.28, C:T.30, C:T.30, C:S.32, C:F.33, C:R.55, C:R.55, C:D.56, C:D.78, C:V.79, C:A.98, C:A.100, C:K.102, C:Y.152, C:K.156, C:V.185, C:S.188, C:S.188, C:S.188 Water bridges: C:G.31, C:G.34, C:S.54, C:K.59, C:K.59, C:R.80, C:R.189, D:D.56 Salt bridges: C:R.55, C:K.59, C:K.102, C:K.102, C:R.189 pi-Cation interactions: C:R.55 NDP.9: 29 residues within 4Å: Chain D: G.28, T.30, G.31, S.32, F.33, S.54, R.55, D.56, K.59, G.77, D.78, V.79, A.98, A.99, A.100, K.102, T.117, L.140, S.141, T.142, Y.152, K.156, Y.182, G.183, N.184, V.185, S.188, R.189 Ligands: UD1.10 35 PLIP interactions: 33 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.182, D:V.185 Hydrogen bonds: D:G.28, D:T.30, D:T.30, D:S.32, D:F.33, D:R.55, D:R.55, D:D.56, D:D.78, D:V.79, D:A.98, D:A.100, D:K.102, D:K.156, D:V.185, D:S.188, D:S.188, D:S.188 Water bridges: D:G.31, D:G.34, D:S.54, D:K.59, D:K.59, D:R.80, D:S.188, C:D.56, C:E.57 Salt bridges: D:R.55, D:K.59, D:K.102, D:K.102, D:R.189 pi-Cation interactions: D:R.55 NDP.13: 29 residues within 4Å: Chain E: G.28, T.30, G.31, S.32, F.33, S.54, R.55, D.56, K.59, G.77, D.78, V.79, A.98, A.99, A.100, K.102, T.117, L.140, S.141, T.142, Y.152, K.156, Y.182, G.183, N.184, V.185, S.188, R.189 Ligands: UD1.14 35 PLIP interactions: 34 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:Y.182, E:V.185 Hydrogen bonds: E:G.28, E:T.30, E:T.30, E:S.32, E:F.33, E:R.55, E:R.55, E:D.56, E:D.78, E:V.79, E:A.98, E:A.100, E:K.102, E:Y.152, E:K.156, E:V.185, E:S.188, E:S.188, E:S.188 Water bridges: E:G.31, E:G.34, E:S.54, E:K.59, E:K.59, E:R.80, E:R.189, F:D.56 Salt bridges: E:R.55, E:K.59, E:K.102, E:K.102, E:R.189 pi-Cation interactions: E:R.55 NDP.15: 29 residues within 4Å: Chain F: G.28, T.30, G.31, S.32, F.33, S.54, R.55, D.56, K.59, G.77, D.78, V.79, A.98, A.99, A.100, K.102, T.117, L.140, S.141, T.142, Y.152, K.156, Y.182, G.183, N.184, V.185, S.188, R.189 Ligands: UD1.16 35 PLIP interactions: 33 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Y.182, F:V.185 Hydrogen bonds: F:G.28, F:T.30, F:T.30, F:S.32, F:F.33, F:R.55, F:R.55, F:D.56, F:D.78, F:V.79, F:A.98, F:A.100, F:K.102, F:K.156, F:V.185, F:S.188, F:S.188, F:S.188 Water bridges: F:G.31, F:G.34, F:S.54, F:K.59, F:K.59, F:R.80, F:S.188, E:D.56, E:E.57 Salt bridges: F:R.55, F:K.59, F:K.102, F:K.102, F:R.189 pi-Cation interactions: F:R.55

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

UD1.2: 21 residues within 4Å: Chain A: K.102, T.142, D.143, K.144, Y.152, G.183, N.184, G.190, S.191, V.192, F.195, F.196, P.208, I.209, T.210, M.214, R.216, M.250, R.269, E.272 Ligands: NDP.1 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:K.102, A:K.102, A:T.142, A:D.143, A:K.144, A:Y.152, A:N.184, A:N.184, A:S.188, A:V.192, A:P.208, A:T.210, A:T.210, A:T.210, A:R.269, A:E.272 Water bridges: A:V.104, A:N.184, A:S.191, A:V.193, A:R.216, A:R.216, A:R.269 Salt bridges: A:K.144, A:K.144, A:R.216, A:R.269 UD1.4: 24 residues within 4Å: Chain B: K.102, H.103, T.142, D.143, K.144, Y.152, G.183, N.184, S.188, R.189, G.190, S.191, V.192, F.195, P.208, I.209, T.210, M.214, R.216, M.250, I.266, R.269, E.272 Ligands: NDP.3 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.192 Hydrogen bonds: B:K.102, B:K.102, B:T.142, B:D.143, B:K.144, B:Y.152, B:Y.152, B:N.184, B:N.184, B:S.188, B:V.192, B:P.208, B:T.210, B:T.210, B:R.269, B:E.272 Water bridges: B:N.184, B:S.191, B:R.216, B:R.216, B:R.269 Salt bridges: B:K.144, B:K.144, B:R.216, B:R.269 UD1.8: 21 residues within 4Å: Chain C: K.102, T.142, D.143, K.144, Y.152, G.183, N.184, G.190, S.191, V.192, F.195, F.196, P.208, I.209, T.210, M.214, R.216, M.250, R.269, E.272 Ligands: NDP.7 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:K.102, C:K.102, C:T.142, C:D.143, C:K.144, C:Y.152, C:N.184, C:N.184, C:S.188, C:V.192, C:P.208, C:T.210, C:T.210, C:T.210, C:R.269, C:E.272 Water bridges: C:V.104, C:N.184, C:S.191, C:V.193, C:R.216, C:R.216, C:R.269 Salt bridges: C:K.144, C:K.144, C:R.216, C:R.269 UD1.10: 24 residues within 4Å: Chain D: K.102, H.103, T.142, D.143, K.144, Y.152, G.183, N.184, S.188, R.189, G.190, S.191, V.192, F.195, P.208, I.209, T.210, M.214, R.216, M.250, I.266, R.269, E.272 Ligands: NDP.9 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:V.192 Hydrogen bonds: D:K.102, D:K.102, D:T.142, D:D.143, D:K.144, D:Y.152, D:Y.152, D:N.184, D:N.184, D:S.188, D:V.192, D:P.208, D:T.210, D:T.210, D:R.269, D:E.272 Water bridges: D:N.184, D:S.191, D:R.216, D:R.216, D:R.269 Salt bridges: D:K.144, D:K.144, D:R.216, D:R.269 UD1.14: 21 residues within 4Å: Chain E: K.102, T.142, D.143, K.144, Y.152, G.183, N.184, G.190, S.191, V.192, F.195, F.196, P.208, I.209, T.210, M.214, R.216, M.250, R.269, E.272 Ligands: NDP.13 27 PLIP interactions: 27 interactions with chain E Hydrogen bonds: E:K.102, E:K.102, E:T.142, E:D.143, E:K.144, E:Y.152, E:N.184, E:N.184, E:S.188, E:V.192, E:P.208, E:T.210, E:T.210, E:T.210, E:R.269, E:E.272 Water bridges: E:V.104, E:N.184, E:S.191, E:V.193, E:R.216, E:R.216, E:R.269 Salt bridges: E:K.144, E:K.144, E:R.216, E:R.269 UD1.16: 24 residues within 4Å: Chain F: K.102, H.103, T.142, D.143, K.144, Y.152, G.183, N.184, S.188, R.189, G.190, S.191, V.192, F.195, P.208, I.209, T.210, M.214, R.216, M.250, I.266, R.269, E.272 Ligands: NDP.15 26 PLIP interactions: 26 interactions with chain F Hydrophobic interactions: F:V.192 Hydrogen bonds: F:K.102, F:K.102, F:T.142, F:D.143, F:K.144, F:Y.152, F:Y.152, F:N.184, F:N.184, F:S.188, F:V.192, F:P.208, F:T.210, F:T.210, F:R.269, F:E.272 Water bridges: F:N.184, F:S.191, F:R.216, F:R.216, F:R.269 Salt bridges: F:K.144, F:K.144, F:R.216, F:R.269

6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 8 residues within 4Å: Chain B: S.123, N.127, S.165 Chain C: N.110, P.111, L.112 Chain D: R.84, Y.87 7 PLIP interactions: 1 interactions with chain B, 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:N.127, C:L.112 Water bridges: D:R.84, D:R.84, D:Y.87, D:Y.87 Salt bridges: D:R.84 MES.6: 8 residues within 4Å: Chain A: R.84, Y.87 Chain B: Y.109, P.111, L.112 Chain C: S.123, N.127, S.165 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:L.112, C:N.127 Salt bridges: A:R.84 MES.11: 8 residues within 4Å: Chain D: S.123, N.127, S.165 Chain E: N.110, P.111, L.112 Chain F: R.84, Y.87 7 PLIP interactions: 5 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Water bridges: F:R.84, F:R.84, F:Y.87, F:Y.87 Salt bridges: F:R.84 Hydrogen bonds: D:N.127, E:L.112 MES.12: 8 residues within 4Å: Chain C: R.84, Y.87 Chain D: Y.109, P.111, L.112 Chain E: S.123, N.127, S.165 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain D Salt bridges: C:R.84 Hydrogen bonds: E:N.127, D:L.112 MES.17: 8 residues within 4Å: Chain A: N.110, P.111, L.112 Chain B: R.84, Y.87 Chain F: S.123, N.127, S.165 7 PLIP interactions: 1 interactions with chain F, 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: F:N.127, A:L.112 Water bridges: B:R.84, B:R.84, B:Y.87, B:Y.87 Salt bridges: B:R.84 MES.18: 8 residues within 4Å: Chain A: S.123, N.127, S.165 Chain E: R.84, Y.87 Chain F: Y.109, P.111, L.112 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:L.112, A:N.127 Salt bridges: E:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishiyama, N. et al., Structural Studies of FlaA1 from Helicobacter pylori Reveal the Mechanism for Inverting 4,6-Dehydratase Activity. J.Biol.Chem. (2006)

Release Date

2006-05-09

Peptides

UDP-GlcNAc C6 dehydratase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

UDP-GlcNAc C6 dehydratase

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