SMTL ID : 5in4.1

Crystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-fucose based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: G.22, T.24, G.25, Q.26, D.27, R.47, N.53, D.78, L.79, L.100, G.101, A.102, S.104, Y.115, V.119, A.145, S.146, T.147, Y.171, K.175, L.198, F.199, N.200, H.201, R.206 Chain B: R.48, S.49, S.50 33 PLIP interactions: 28 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.22, A:T.24, A:T.24, A:T.24, A:G.25, A:Q.26, A:Q.26, A:D.27, A:N.53, A:D.78, A:L.79, A:L.100, A:A.102, A:S.104, A:Y.171, A:K.175, A:H.201, A:H.201, A:R.206, B:S.50 Water bridges: A:G.22, A:I.23, A:G.28, A:R.47, A:R.47, A:R.206, A:G.207, B:R.48, B:S.51, B:S.51 Salt bridges: A:R.47, B:R.48 pi-Cation interactions: A:R.47 NAP.5: 29 residues within 4Å: Chain A: R.48, S.49, S.50 Chain B: G.22, I.23, T.24, G.25, Q.26, D.27, R.47, N.53, D.78, L.79, L.100, G.101, A.102, S.104, Y.115, V.119, A.145, S.146, T.147, Y.171, K.175, L.198, F.199, N.200, H.201, R.206 33 PLIP interactions: 28 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.22, B:T.24, B:T.24, B:T.24, B:G.25, B:Q.26, B:Q.26, B:D.27, B:N.53, B:D.78, B:L.79, B:L.100, B:A.102, B:S.104, B:Y.115, B:K.175, B:H.201, B:H.201, B:R.206, B:R.206, A:S.50 Water bridges: B:I.23, B:G.28, B:R.47, B:R.47, B:R.56, B:G.207, A:R.48, A:S.51, A:S.51 Salt bridges: B:R.47, A:R.48 pi-Cation interactions: B:R.47 NAP.7: 28 residues within 4Å: Chain C: G.22, T.24, G.25, Q.26, D.27, R.47, N.53, D.78, L.79, L.100, G.101, A.102, S.104, Y.115, V.119, A.145, S.146, T.147, Y.171, K.175, L.198, F.199, N.200, H.201, R.206 Chain D: R.48, S.49, S.50 35 PLIP interactions: 30 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.22, C:T.24, C:T.24, C:T.24, C:G.25, C:Q.26, C:Q.26, C:D.27, C:D.27, C:N.53, C:D.78, C:L.79, C:L.100, C:A.102, C:S.104, C:Y.171, C:K.175, C:H.201, C:H.201, C:R.206, C:R.206, D:S.50 Water bridges: C:G.22, C:I.23, C:G.28, C:R.47, C:R.47, C:R.56, C:G.207, D:R.48, D:S.51, D:S.51 Salt bridges: C:R.47, D:R.48 pi-Cation interactions: C:R.47 NAP.11: 28 residues within 4Å: Chain C: R.48, S.49, S.50 Chain D: G.22, T.24, G.25, Q.26, D.27, R.47, N.53, D.78, L.79, L.100, G.101, A.102, S.104, Y.115, V.119, A.145, S.146, T.147, Y.171, K.175, L.198, F.199, N.200, H.201, R.206 36 PLIP interactions: 5 interactions with chain C, 31 interactions with chain D Hydrogen bonds: C:S.50, D:G.22, D:T.24, D:T.24, D:T.24, D:G.25, D:Q.26, D:Q.26, D:D.27, D:D.27, D:N.53, D:D.78, D:L.79, D:L.100, D:A.102, D:S.104, D:Y.115, D:K.175, D:H.201, D:H.201, D:R.206 Water bridges: C:R.48, C:S.51, C:S.51, D:G.22, D:I.23, D:G.28, D:R.47, D:R.47, D:R.56, D:T.147, D:G.207 Salt bridges: C:R.48, D:R.47 Hydrophobic interactions: D:L.198 pi-Cation interactions: D:R.47

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

GDP.2: 18 residues within 4Å: Chain A: H.105, V.106, E.149, N.200, N.209, F.210, V.211, K.214, L.232, G.233, N.234, A.237, R.239, V.273, Y.315, R.317, E.320, V.321 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.149, A:N.200, A:N.209, A:N.209, A:V.211, A:K.214, A:G.233, A:N.234, A:R.317, A:R.317, A:V.321 Water bridges: A:R.206, A:R.206, A:R.206, A:R.317, A:R.317, A:R.317, A:R.317 Salt bridges: A:R.239, A:R.317, A:R.317 GDP.6: 18 residues within 4Å: Chain B: H.105, V.106, E.149, N.200, N.209, F.210, V.211, K.214, L.232, G.233, N.234, A.237, R.239, V.273, Y.315, R.317, E.320, V.321 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:E.149, B:N.200, B:N.209, B:V.211, B:K.214, B:G.233, B:N.234, B:R.317, B:R.317, B:V.321 Water bridges: B:H.105, B:R.206, B:R.206, B:R.206, B:N.209, B:T.212, B:K.214, B:R.239, B:R.239, B:R.317, B:R.317 Salt bridges: B:R.239, B:R.317, B:R.317 GDP.8: 18 residues within 4Å: Chain C: H.105, V.106, E.149, N.200, N.209, F.210, V.211, K.214, L.232, G.233, N.234, A.237, R.239, V.273, Y.315, R.317, E.320, V.321 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:E.149, C:E.149, C:N.200, C:N.209, C:N.209, C:V.211, C:K.214, C:G.233, C:N.234, C:R.317, C:R.317, C:V.321 Water bridges: C:R.206, C:R.206, C:R.206, C:R.239, C:R.317, C:R.317 Salt bridges: C:R.239, C:R.317, C:R.317 GDP.12: 18 residues within 4Å: Chain D: H.105, V.106, E.149, N.200, N.209, F.210, V.211, K.214, L.232, G.233, N.234, A.237, R.239, V.273, Y.315, R.317, E.320, V.321 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:E.149, D:N.200, D:N.209, D:N.209, D:V.211, D:K.214, D:G.233, D:N.234, D:R.317, D:R.317, D:V.321 Water bridges: D:R.206, D:R.206, D:R.239, D:R.317, D:R.317, D:R.317, D:R.317 Salt bridges: D:R.239, D:R.317, D:R.317

4 x 6CK: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(trifluoromethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)(Non-covalent)

6CK.3: 14 residues within 4Å: Chain A: F.52, T.54, Y.61, A.66, H.67, E.69, L.74, Y.76 Chain B: A.208, N.209, K.214, R.217, Y.315, A.364 21 PLIP interactions: 13 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.54, A:T.54, A:Y.61, A:Y.61, A:H.67, A:E.69, A:L.74, A:Y.76, B:N.209, B:R.217, B:Y.315, B:A.364 Water bridges: A:E.69, B:N.209, B:K.214, B:A.364 pi-Stacking: A:F.52, A:F.52, A:H.67 pi-Cation interactions: A:H.67 Salt bridges: B:K.214 6CK.4: 15 residues within 4Å: Chain A: A.208, N.209, K.214, R.217, Y.315, A.364 Chain B: V.46, F.52, T.54, Y.61, A.66, H.67, E.69, L.74, Y.76 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.54, B:Y.61, B:Y.61, B:A.66, B:H.67, B:L.74, A:N.209, A:R.217, A:Y.315, A:Y.315, A:A.364 Water bridges: B:T.54, B:T.54, A:R.217, A:Y.315 pi-Stacking: B:F.52, B:F.52, B:H.67 pi-Cation interactions: B:H.67 Salt bridges: A:K.214 6CK.9: 15 residues within 4Å: Chain C: F.52, T.54, Y.61, A.66, H.67, E.69, L.74, Y.76 Chain D: A.208, N.209, K.214, R.217, Y.315, N.363, A.364 20 PLIP interactions: 8 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:N.209, D:R.217, D:Y.315, D:A.364, C:T.54, C:Y.61, C:Y.61, C:H.67, C:L.74, C:Y.76 Water bridges: D:H.105, D:A.364, D:A.364, C:T.54, C:T.54 Salt bridges: D:K.214 pi-Stacking: C:F.52, C:F.52, C:H.67 pi-Cation interactions: C:H.67 6CK.10: 15 residues within 4Å: Chain C: A.208, N.209, K.214, R.217, Y.315, N.363, A.364 Chain D: F.52, T.54, Y.61, A.66, H.67, E.69, L.74, Y.76 25 PLIP interactions: 14 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:T.54, D:Y.61, D:Y.61, D:A.66, D:H.67, D:E.69, D:L.74, C:N.209, C:R.217, C:Y.315, C:A.364 Water bridges: D:T.54, D:T.54, D:E.69, C:H.105, C:N.209, C:K.214, C:Y.315, C:A.364, C:A.364 pi-Stacking: D:F.52, D:F.52, D:H.67 pi-Cation interactions: D:H.67 Salt bridges: C:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allen, J.G. et al., Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase. Acs Chem.Biol. (2016)

Release Date

2016-08-17

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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