SMTL ID : 1rpn.5 (4 other biounits)

Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 27 residues within 4Å: Chain A: G.21, T.23, G.24, Q.25, D.26, A.46, R.48, D.71, M.72, L.93, A.94, A.95, S.97, V.112, A.136, S.137, T.138, Y.162, K.166, L.189, F.190, N.191, H.192, R.197 Chain D: R.47, R.48, S.49 33 PLIP interactions: 29 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.189 Hydrogen bonds: A:G.21, A:T.23, A:Q.25, A:Q.25, A:D.26, A:R.48, A:D.71, A:M.72, A:L.93, A:A.95, A:S.97, A:Y.162, A:K.166, A:H.192, A:H.192, A:R.197, A:R.197, D:S.49 Water bridges: A:G.21, A:T.23, A:T.23, A:G.24, A:G.27, A:A.46, A:T.52, A:G.198, D:R.47, D:S.50 Salt bridges: A:R.48, D:R.47 pi-Cation interactions: A:R.48, A:R.48 NDP.3: 27 residues within 4Å: Chain B: G.21, T.23, G.24, Q.25, D.26, A.46, R.48, D.71, M.72, L.93, A.94, A.95, S.97, V.112, A.136, S.137, T.138, Y.162, K.166, L.189, F.190, N.191, H.192, R.197 Chain C: R.47, R.48, S.49 34 PLIP interactions: 29 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.189 Hydrogen bonds: B:G.21, B:T.23, B:T.23, B:Q.25, B:Q.25, B:D.26, B:D.26, B:R.48, B:D.71, B:M.72, B:L.93, B:A.95, B:S.97, B:K.166, B:H.192, B:H.192, B:R.197, B:R.197, C:R.48, C:S.49 Water bridges: B:I.22, B:T.23, B:G.24, B:G.24, B:A.46, B:T.52, B:G.198, C:R.47, C:S.50 Salt bridges: B:R.48, C:R.47 pi-Cation interactions: B:R.48, B:R.48 NDP.5: 27 residues within 4Å: Chain B: R.47, R.48, S.49 Chain C: G.21, T.23, G.24, Q.25, D.26, A.46, R.48, D.71, M.72, L.93, A.94, A.95, S.97, V.112, A.136, S.137, T.138, Y.162, K.166, L.189, F.190, N.191, H.192, R.197 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.189 Hydrogen bonds: C:G.21, C:T.23, C:T.23, C:Q.25, C:Q.25, C:D.26, C:D.26, C:R.48, C:D.71, C:M.72, C:L.93, C:A.95, C:S.97, C:K.166, C:H.192, C:H.192, C:R.197, C:R.197, B:R.48, B:S.49 Water bridges: C:I.22, C:T.23, C:G.24, C:G.24, C:A.46, C:T.52, C:G.198, B:R.47, B:S.50 Salt bridges: C:R.48, B:R.47 pi-Cation interactions: C:R.48, C:R.48 NDP.7: 27 residues within 4Å: Chain A: R.47, R.48, S.49 Chain D: G.21, T.23, G.24, Q.25, D.26, A.46, R.48, D.71, M.72, L.93, A.94, A.95, S.97, V.112, A.136, S.137, T.138, Y.162, K.166, L.189, F.190, N.191, H.192, R.197 37 PLIP interactions: 30 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:L.189 Hydrogen bonds: D:G.21, D:T.23, D:Q.25, D:Q.25, D:D.26, D:R.48, D:D.71, D:M.72, D:A.94, D:A.95, D:S.97, D:Y.162, D:K.166, D:H.192, D:H.192, D:R.197, D:R.197, A:R.48, A:S.49, A:S.49 Water bridges: D:I.22, D:T.23, D:T.23, D:G.24, D:G.27, D:A.46, D:T.52, D:T.52, D:G.198, A:R.47, A:S.49, A:S.50 Salt bridges: D:R.48, A:R.47 pi-Cation interactions: D:R.48, D:R.48

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

GDP.2: 19 residues within 4Å: Chain A: F.98, V.99, E.140, N.191, E.200, F.201, V.202, K.205, R.222, L.223, G.224, N.225, A.228, R.230, V.264, F.289, R.291, E.294, V.295 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:E.140, A:E.140, A:N.191, A:E.200, A:E.200, A:V.202, A:K.205, A:G.224, A:N.225, A:R.291, A:R.291, A:V.295 Water bridges: A:E.140, A:E.140, A:E.140, A:R.197, A:R.197, A:R.197, A:R.291, A:R.291 Salt bridges: A:R.230, A:R.291, A:R.291 GDP.4: 19 residues within 4Å: Chain B: F.98, V.99, E.140, N.191, E.200, F.201, V.202, K.205, R.222, L.223, G.224, N.225, A.228, R.230, V.264, F.289, R.291, E.294, V.295 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.140, B:E.140, B:N.191, B:E.200, B:E.200, B:V.202, B:K.205, B:G.224, B:R.291, B:R.291, B:V.295 Water bridges: B:R.197, B:R.197, B:R.197, B:N.225, B:R.291, B:R.291 Salt bridges: B:R.230, B:R.291, B:R.291 GDP.6: 19 residues within 4Å: Chain C: F.98, V.99, E.140, N.191, E.200, F.201, V.202, K.205, R.222, L.223, G.224, N.225, A.228, R.230, V.264, F.289, R.291, E.294, V.295 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:E.140, C:E.140, C:N.191, C:E.200, C:E.200, C:V.202, C:K.205, C:G.224, C:R.291, C:R.291, C:V.295 Water bridges: C:R.197, C:N.225, C:R.230, C:R.291 Salt bridges: C:R.230, C:R.291, C:R.291 GDP.8: 19 residues within 4Å: Chain D: F.98, V.99, E.140, N.191, E.200, F.201, V.202, K.205, R.222, L.223, G.224, N.225, A.228, R.230, V.264, F.289, R.291, E.294, V.295 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:E.140, D:E.140, D:N.191, D:E.200, D:E.200, D:V.202, D:K.205, D:G.224, D:R.291, D:R.291, D:V.295 Water bridges: D:E.140, D:E.140, D:E.140, D:R.197, D:N.225, D:R.230, D:R.291, D:R.291 Salt bridges: D:R.230, D:R.291, D:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Webb, N.A. et al., Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway. Protein Sci. (2004)

Release Date

2004-02-24

Peptides

GDP-mannose 4,6-dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GDP-mannose 4,6-dehydratase

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