SMTL ID : 7us5.1

X-ray crystal structure of GDP-D-glycero-D-manno-heptose 4,6-Dehydratase from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.30, T.32, G.33, Q.34, V.35, M.54, R.56, E.59, D.83, L.84, N.85, L.105, A.106, A.107, S.109, T.124, C.152, S.153, S.154, Y.179, K.183, M.206, G.207, T.208, H.209, R.214, S.215 Chain B: Q.58 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.206 Hydrogen bonds: A:G.30, A:T.32, A:G.33, A:Q.34, A:Q.34, A:V.35, A:R.56, A:D.83, A:L.84, A:L.105, A:A.107, A:S.109, A:Y.179, A:K.183, A:H.209, A:H.209, A:R.214, B:Q.58 Water bridges: A:G.30, A:T.32, A:G.36, A:R.56, A:N.85, A:S.109, A:R.214, A:S.215, B:Q.58 pi-Cation interactions: A:R.56, A:R.56 NAD.4: 28 residues within 4Å: Chain A: Q.58 Chain B: G.30, T.32, G.33, Q.34, V.35, M.54, R.56, E.59, D.83, L.84, N.85, L.105, A.106, A.107, S.109, T.124, C.152, S.153, S.154, Y.179, K.183, M.206, G.207, T.208, H.209, R.214, S.215 30 PLIP interactions: 29 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.30, B:T.32, B:T.32, B:T.32, B:G.33, B:Q.34, B:Q.34, B:V.35, B:R.56, B:R.56, B:D.83, B:L.84, B:L.105, B:A.107, B:S.109, B:K.183, B:H.209, B:H.209, B:R.214, A:Q.58 Water bridges: B:F.31, B:G.36, B:N.85, B:N.85, B:S.109, B:R.214, B:R.214, B:S.215 pi-Cation interactions: B:R.56, B:R.56 NAD.7: 28 residues within 4Å: Chain C: G.30, T.32, G.33, Q.34, V.35, M.54, R.56, E.59, D.83, L.84, N.85, L.105, A.106, A.107, S.109, T.124, C.152, S.153, S.154, Y.179, K.183, M.206, G.207, T.208, H.209, R.214, S.215 Chain D: Q.58 33 PLIP interactions: 31 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:M.206 Hydrogen bonds: C:G.30, C:T.32, C:T.32, C:G.33, C:Q.34, C:Q.34, C:V.35, C:R.56, C:D.83, C:L.84, C:N.85, C:L.105, C:A.107, C:S.109, C:K.183, C:H.209, C:H.209, C:R.214, C:S.215, D:Q.58 Water bridges: C:F.31, C:T.32, C:G.36, C:R.56, C:R.56, C:S.109, C:T.124, C:R.214, C:S.215, D:Q.58 pi-Cation interactions: C:R.56, C:R.56 NAD.12: 28 residues within 4Å: Chain C: Q.58 Chain D: G.30, T.32, G.33, Q.34, V.35, M.54, R.56, E.59, D.83, L.84, N.85, L.105, A.106, A.107, S.109, T.124, C.152, S.153, S.154, Y.179, K.183, M.206, G.207, T.208, H.209, R.214, S.215 31 PLIP interactions: 30 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:M.206 Hydrogen bonds: D:G.30, D:T.32, D:T.32, D:G.33, D:Q.34, D:Q.34, D:V.35, D:R.56, D:D.83, D:L.84, D:L.105, D:A.107, D:S.109, D:Y.179, D:K.183, D:H.209, D:H.209, D:R.214, D:S.215, D:S.215, C:Q.58 Water bridges: D:G.30, D:G.36, D:R.56, D:N.85, D:S.109, D:T.124, D:R.214 pi-Cation interactions: D:R.56, D:R.56

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 16 residues within 4Å: Chain A: Y.110, P.111, E.156, V.217, F.218, F.219, T.222, V.241, G.242, N.243, S.246, R.248, L.288, R.313, R.315, D.318 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:E.156, A:E.156, A:V.217, A:V.217, A:F.219, A:G.242, A:S.246, A:S.246, A:R.313, A:R.315, A:R.315 Water bridges: A:R.214, A:R.214, A:R.214, A:N.243, A:R.248, A:R.315, A:R.315 Salt bridges: A:R.248, A:R.315, A:R.315 pi-Stacking: A:F.219 GDP.5: 16 residues within 4Å: Chain B: Y.110, P.111, E.156, V.217, F.218, F.219, T.222, V.241, G.242, N.243, S.246, R.248, L.288, R.313, R.315, D.318 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:Y.110, B:E.156, B:V.217, B:V.217, B:F.219, B:G.242, B:S.246, B:R.248, B:R.313, B:R.315, B:R.315, B:A.319 Water bridges: B:R.214, B:R.214, B:R.214, B:R.214, B:T.222, B:T.222, B:R.248, B:R.248, B:R.248, B:R.248, B:R.315, B:A.319 Salt bridges: B:R.248, B:R.315, B:R.315 pi-Stacking: B:F.219 GDP.8: 16 residues within 4Å: Chain C: Y.110, P.111, E.156, V.217, F.218, F.219, T.222, V.241, G.242, N.243, S.246, R.248, L.288, R.313, R.315, D.318 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:Y.110, C:E.156, C:E.156, C:V.217, C:V.217, C:F.219, C:G.242, C:S.246, C:S.246, C:R.313, C:R.315, C:R.315 Water bridges: C:R.214, C:R.214, C:R.214, C:R.214, C:T.222, C:T.222, C:N.243, C:R.315, C:R.315, C:R.315 Salt bridges: C:R.248, C:R.315, C:R.315 pi-Stacking: C:F.219 GDP.13: 16 residues within 4Å: Chain D: Y.110, P.111, E.156, V.217, F.218, F.219, T.222, V.241, G.242, N.243, S.246, R.248, L.288, R.313, R.315, D.318 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:E.156, D:E.156, D:V.217, D:V.217, D:F.219, D:G.242, D:S.246, D:R.313, D:R.315, D:R.315, D:A.319 Water bridges: D:R.214, D:R.214, D:R.214, D:N.243, D:R.315, D:R.315 Salt bridges: D:R.248, D:R.315, D:R.315 pi-Stacking: D:F.219

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: Y.110, K.112, V.217, R.365 Chain B: Y.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.110, A:R.365 EDO.6: 4 residues within 4Å: Chain A: Y.81 Chain B: Y.110, K.112, R.365 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.365 Water bridges: B:Y.110 EDO.9: 4 residues within 4Å: Chain C: Y.110, K.112, R.365 Chain D: Y.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.365 Water bridges: C:Y.110, C:Y.110, C:R.365 EDO.10: 3 residues within 4Å: Chain C: P.60, D.62, N.63 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Water bridges: C:D.62, C:N.63, C:N.63, C:D.216, D:Q.58 EDO.11: 8 residues within 4Å: Chain C: R.56, Q.58, E.59, P.60 Chain D: R.56, Q.58, E.59, P.60 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.56, D:Q.58, C:R.56, C:Q.58 EDO.14: 4 residues within 4Å: Chain C: Y.81 Chain D: Y.110, K.112, R.365 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.110, D:R.365, D:R.365

Links

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Citation

Xiang, D.F. et al., Reaction Mechanism and Three-Dimensional Structure of GDP-d-glycero-alpha-d-manno-heptose 4,6-Dehydratase from Campylobacter jejuni. Biochemistry (2022)

Release Date

2022-07-06

Peptides

GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE