SMTL ID : 5in5.1

Crystal Structure of GDP-mannose 4,6 dehydratase in complex with natural inhibitor GDP-Fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 29 residues within 4Å: Chain A: 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 Chain B: R.48, S.49, S.50 33 PLIP interactions: 29 interactions with chain A, 4 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.115, A:K.175, A:H.201, A:H.201, A:R.206, A:R.206, B:S.50 Water bridges: A:G.22, A:G.22, A:I.23, A:G.28, A:R.47, A:R.47, A:G.207, B:S.51, B:S.51 Salt bridges: A:R.47, B:R.48 pi-Cation interactions: A:R.47 NAP.6: 30 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, Q.103, 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: 29 interactions with chain B, 4 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:Y.171, B:K.175, B:H.201, B:H.201, B:R.206, B:R.206, A:S.50 Water bridges: B:G.22, B:I.23, B:G.28, B:R.47, B:R.47, B:G.207, A:S.50, A:S.51 Salt bridges: B:R.47, A:R.48 pi-Cation interactions: B:R.47 NAP.8: 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 34 PLIP interactions: 29 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.115, 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: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.12: 30 residues within 4Å: Chain C: R.48, S.49, S.50 Chain D: 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, Q.103, 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 34 PLIP interactions: 29 interactions with chain D, 5 interactions with chain C Hydrogen bonds: 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.171, D:K.175, D:H.201, D:H.201, D:R.206, D:R.206, C:S.50 Water bridges: D:G.22, D:I.23, D:G.28, D:R.47, D:R.47, D:G.207, C:R.48, C:R.48, C:S.51 Salt bridges: D:R.47, C:R.48 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 19 PLIP interactions: 19 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:E.149, A:R.206, A:R.206, A:R.206, A:R.239 Salt bridges: A:R.239, A:R.317, A:R.317 GDP.7: 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 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:E.149, B:E.149, B:N.200, B:N.209, 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:E.149, B:E.149, B:E.149, B:R.206, B:R.206, B:R.239, B:R.317 Salt bridges: B:R.239, B:R.317, B:R.317 GDP.9: 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 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: 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:E.149, C:R.206, C:R.206, C:R.206, C:R.239, C:R.317 Salt bridges: C:R.239, C:R.317, C:R.317 GDP.13: 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 20 PLIP interactions: 20 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:E.149, D:R.206, D:R.206, D:R.206, D:R.239, D:R.317 Salt bridges: D:R.239, D:R.317, D:R.317

4 x GFB: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE(Non-covalent)

GFB.3: 15 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, N.363, A.364 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:N.209, B:R.217, B:Y.315, B:A.364, A:T.54, A:T.54, A:Y.61, A:A.66, A:H.67, A:H.67, A:E.69, A:E.69 Water bridges: B:Y.315 Salt bridges: B:K.214 Hydrophobic interactions: A:L.74 pi-Stacking: A:F.52, A:F.52, A:H.67 pi-Cation interactions: A:H.67 GFB.5: 16 residues within 4Å: Chain A: A.208, N.209, K.214, R.217, Y.315, N.363, A.364 Chain B: F.52, T.54, E.58, Y.61, A.66, H.67, E.69, L.74, Y.76 21 PLIP interactions: 13 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.74 Hydrogen bonds: B:T.54, B:T.54, B:Y.61, B:A.66, B:H.67, B:E.69, B:Y.76, A:N.209, A:R.217, A:S.218, A:Y.315, A:Y.315, A:A.364 Salt bridges: B:E.58, A:K.214 pi-Stacking: B:F.52, B:F.52, B:H.67 pi-Cation interactions: B:H.67 Water bridges: A:K.214 GFB.10: 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 19 PLIP interactions: 6 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:N.209, D:R.217, D:Y.315, D:Y.315, D:A.364, C:T.54, C:Y.61, C:A.66, C:H.67, C:H.67, C:E.69 Salt bridges: D:K.214 Hydrophobic interactions: C:L.74 Water bridges: C:E.69, C:L.74 pi-Stacking: C:F.52, C:F.52, C:H.67 pi-Cation interactions: C:H.67 GFB.11: 17 residues within 4Å: Chain C: A.208, N.209, K.214, R.217, Y.315, N.363, A.364 Chain D: V.46, F.52, T.54, E.58, Y.61, A.66, H.67, E.69, L.74, Y.76 24 PLIP interactions: 9 interactions with chain C, 15 interactions with chain D Hydrogen bonds: C:N.209, C:R.217, C:Y.315, C:A.364, D:T.54, D:T.54, D:Y.61, D:A.66, D:H.67, D:E.69, D:E.69, D:Y.76 Water bridges: C:Y.315, C:Y.315, C:Y.315, C:A.364 Salt bridges: C:K.214, D:E.58 Hydrophobic interactions: D:V.46, D:L.74 pi-Stacking: D:F.52, D:F.52, D:H.67 pi-Cation interactions: D:H.67

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Y.223, H.283, H.352 No protein-ligand interaction detected (PLIP)

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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