SMTL ID : 1n7h.1

Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 28 residues within 4Å: Chain A: G.35, I.36, T.37, G.38, Q.39, D.40, R.60, D.91, L.92, L.113, A.114, A.115, S.117, Y.128, V.132, A.160, G.161, S.162, Y.185, K.189, L.212, F.213, N.214, H.215, R.220 Chain D: R.61, S.62, S.63 34 PLIP interactions: 28 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:G.35, A:T.37, A:T.37, A:T.37, A:G.38, A:Q.39, A:Q.39, A:D.40, A:D.40, A:N.66, A:D.91, A:L.92, A:L.113, A:A.115, A:S.117, A:Y.128, A:K.189, A:H.215, A:H.215, A:R.220, A:R.220, D:S.63 Water bridges: A:G.35, A:G.41, A:R.60, A:R.60, A:G.221, D:R.61, D:S.63, D:N.64, D:N.64 Salt bridges: A:R.60, D:R.61 pi-Cation interactions: A:R.60 NDP.3: 29 residues within 4Å: Chain B: G.35, I.36, T.37, G.38, Q.39, D.40, R.60, N.66, D.91, L.92, L.113, A.114, A.115, S.117, Y.128, V.132, A.160, G.161, S.162, Y.185, K.189, L.212, F.213, N.214, H.215, R.220 Chain C: R.61, S.62, S.63 33 PLIP interactions: 27 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.35, B:T.37, B:T.37, B:T.37, B:G.38, B:Q.39, B:Q.39, B:D.40, B:N.66, B:D.91, B:L.92, B:L.113, B:A.115, B:S.117, B:Y.128, B:K.189, B:H.215, B:H.215, B:R.220, B:R.220, C:S.63 Water bridges: B:G.35, B:G.41, B:R.60, B:R.60, B:G.221, C:R.61, C:R.61, C:N.64, C:N.64 Salt bridges: B:R.60, C:R.61 pi-Cation interactions: B:R.60 NDP.5: 28 residues within 4Å: Chain B: R.61, S.62, S.63 Chain C: G.35, I.36, T.37, G.38, Q.39, D.40, R.60, D.91, L.92, L.113, A.114, A.115, S.117, Y.128, V.132, A.160, G.161, S.162, Y.185, K.189, L.212, F.213, N.214, H.215, R.220 34 PLIP interactions: 28 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:G.35, C:T.37, C:T.37, C:T.37, C:G.38, C:Q.39, C:Q.39, C:D.40, C:N.66, C:D.91, C:L.92, C:L.113, C:A.115, C:S.117, C:Y.128, C:Y.185, C:K.189, C:H.215, C:H.215, C:R.220, C:R.220, B:S.63 Water bridges: C:G.35, C:G.41, C:R.60, C:R.60, C:G.221, B:R.61, B:S.63, B:N.64, B:N.64 Salt bridges: C:R.60, B:R.61 pi-Cation interactions: C:R.60 NDP.7: 29 residues within 4Å: Chain A: R.61, S.62, S.63 Chain D: G.35, I.36, T.37, G.38, Q.39, D.40, R.60, N.66, D.91, L.92, L.113, A.114, A.115, S.117, Y.128, V.132, A.160, G.161, S.162, Y.185, K.189, L.212, F.213, N.214, H.215, R.220 35 PLIP interactions: 29 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:G.35, D:T.37, D:T.37, D:T.37, D:G.38, D:Q.39, D:Q.39, D:D.40, D:D.40, D:N.66, D:D.91, D:L.92, D:L.113, D:A.115, D:S.117, D:Y.128, D:Y.185, D:K.189, D:H.215, D:H.215, D:R.220, D:R.220, A:S.63 Water bridges: D:G.35, D:G.41, D:R.60, D:R.60, D:G.221, A:R.61, A:R.61, A:N.64, A:N.64 Salt bridges: D:R.60, A:R.61 pi-Cation interactions: D:R.60

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

GDP.2: 18 residues within 4Å: Chain A: H.118, V.119, E.164, N.214, N.223, F.224, V.225, K.228, F.245, L.246, G.247, N.248, A.251, R.253, V.287, Y.312, R.314, E.317 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:H.118, A:E.164, A:N.214, A:N.223, A:V.225, A:K.228, A:G.247, A:N.248, A:R.314, A:R.314 Water bridges: A:R.220, A:R.220, A:R.220, A:R.253, A:R.314, A:R.314 Salt bridges: A:R.253, A:R.314, A:R.314 GDP.4: 18 residues within 4Å: Chain B: H.118, V.119, E.164, N.214, N.223, F.224, V.225, K.228, F.245, L.246, G.247, N.248, A.251, R.253, V.287, Y.312, R.314, E.317 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:H.118, B:E.164, B:N.214, B:N.223, B:V.225, B:K.228, B:G.247, B:N.248, B:R.314, B:R.314, B:V.318 Water bridges: B:E.164, B:E.164, B:E.164, B:R.220, B:R.220, B:R.220, B:R.253, B:R.314, B:R.314 Salt bridges: B:R.253, B:R.314, B:R.314 GDP.6: 18 residues within 4Å: Chain C: H.118, V.119, E.164, N.214, N.223, F.224, V.225, K.228, F.245, L.246, G.247, N.248, A.251, R.253, V.287, Y.312, R.314, E.317 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:H.118, C:E.164, C:N.214, C:N.223, C:V.225, C:K.228, C:G.247, C:N.248, C:R.314, C:R.314 Water bridges: C:E.164, C:E.164, C:E.164, C:R.220, C:R.220, C:R.220, C:R.253, C:R.314, C:R.314 Salt bridges: C:R.253, C:R.314, C:R.314 GDP.8: 18 residues within 4Å: Chain D: H.118, V.119, E.164, N.214, N.223, F.224, V.225, K.228, F.245, L.246, G.247, N.248, A.251, R.253, V.287, Y.312, R.314, E.317 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:H.118, D:E.164, D:N.214, D:N.223, D:V.225, D:K.228, D:G.247, D:N.248, D:R.314, D:R.314, D:V.318 Water bridges: D:R.220, D:R.220, D:R.220, D:R.253, D:R.314, D:R.314 Salt bridges: D:R.253, D:R.314, D:R.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mulichak, A.M. et al., The structure of the MUR1 GDP-mannose 4,6-dehydratase from A. thaliana: Implications for ligand binding and specificity. Biochemistry (2002)

Release Date

2003-01-07

Peptides

GDP-D-mannose-4,6-dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

GDP-D-mannose-4,6-dehydratase

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