SMTL ID : 6gpl.1

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

1 x BCN: BICINE(Non-covalent)

BCN.1: 10 residues within 4Å: Chain A: R.44, R.193, R.194, G.195, A.196, R.201, L.345 Chain D: S.38, S.39, F.40 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:F.40, A:A.196, A:R.201, A:R.201 Water bridges: A:N.197

4 x F7E: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},6~{R})-6-methyl-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate(Non-covalent)

F7E.2: 25 residues within 4Å: Chain A: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, L.186, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, V.261, Y.303, R.305, E.308, V.309 Ligands: NAP.3 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:S.92, A:Y.159, A:N.188, A:R.194, A:R.194, A:N.197, A:V.199, A:K.202, A:G.221, A:N.222, A:R.305, A:E.308 Water bridges: A:S.92, A:H.93, A:N.197, A:N.197, A:K.202, A:R.227, A:R.227, A:Y.303, A:R.305, A:E.308 Salt bridges: A:R.194, A:R.227, A:R.305, A:R.305 F7E.8: 25 residues within 4Å: Chain B: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, L.186, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, V.261, Y.303, R.305, E.308, V.309 Ligands: NAP.9 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:S.92, B:Y.159, B:N.188, B:R.194, B:R.194, B:N.197, B:V.199, B:K.202, B:G.221, B:N.222, B:R.305, B:E.308 Water bridges: B:S.92, B:H.93, B:N.197, B:N.197, B:K.202, B:R.227, B:Y.303, B:R.305, B:R.305, B:E.308 Salt bridges: B:R.194, B:R.227, B:R.305, B:R.305 F7E.12: 25 residues within 4Å: Chain C: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, L.186, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, V.261, Y.303, R.305, E.308, V.309 Ligands: NAP.13 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:S.92, C:T.135, C:N.188, C:R.194, C:R.194, C:N.197, C:V.199, C:K.202, C:G.221, C:N.222, C:R.305, C:E.308 Water bridges: C:S.92, C:H.93, C:E.137, C:N.197, C:N.197, C:K.202, C:R.227, C:R.227, C:Y.303, C:R.305, C:E.308 Salt bridges: C:R.194, C:R.227, C:R.305, C:R.305 F7E.17: 25 residues within 4Å: Chain D: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, L.186, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, V.261, Y.303, R.305, E.308, V.309 Ligands: NAP.18 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:S.92, D:T.135, D:N.188, D:R.194, D:R.194, D:N.197, D:V.199, D:K.202, D:G.221, D:N.222, D:R.305, D:E.308 Water bridges: D:S.92, D:E.137, D:E.137, D:N.197, D:K.202, D:R.227, D:Y.303, D:R.305, D:R.305, D:E.308 Salt bridges: D:R.194, D:R.227, D:R.305, D:R.305

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

NAP.3: 31 residues within 4Å: Chain A: G.10, I.11, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, L.88, G.89, A.90, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163, L.186, F.187, N.188, H.189, R.194 Chain D: R.36, S.37, S.38 Ligands: F7E.2, EDO.6 33 PLIP interactions: 28 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:L.186 Hydrogen bonds: A:G.10, A:T.12, A:T.12, A:T.12, A:G.13, A:Q.14, A:Q.14, A:D.15, A:N.41, A:D.66, A:L.67, A:L.88, A:A.90, A:S.92, A:Y.103, A:K.163, A:H.189, A:H.189, A:R.194, A:R.194, D:S.38 Water bridges: A:G.10, A:I.11, A:G.16, A:R.35, A:R.44, D:R.36, D:S.38, D:S.39 Salt bridges: A:R.35, D:R.36 pi-Cation interactions: A:R.35 NAP.9: 31 residues within 4Å: Chain B: G.10, I.11, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, L.88, G.89, A.90, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163, L.186, F.187, N.188, H.189, R.194 Chain C: R.36, S.37, S.38 Ligands: F7E.8, EDO.14 31 PLIP interactions: 26 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.186 Hydrogen bonds: B:G.10, B:T.12, B:T.12, B:G.13, B:Q.14, B:Q.14, B:D.15, B:N.41, B:D.66, B:L.67, B:L.88, B:A.90, B:S.92, B:Y.103, B:K.163, B:H.189, B:H.189, B:R.194, B:R.194, C:S.38, C:S.38 Water bridges: B:I.11, B:G.16, B:R.35, B:G.195, C:S.38, C:S.39 Salt bridges: B:R.35, C:R.36 pi-Cation interactions: B:R.35 NAP.13: 31 residues within 4Å: Chain B: R.36, S.37, S.38 Chain C: G.10, I.11, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, L.88, G.89, A.90, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163, L.186, F.187, N.188, H.189, R.194 Ligands: F7E.12, EDO.14 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.186 Hydrogen bonds: C:G.10, C:T.12, C:T.12, C:T.12, C:G.13, C:Q.14, C:Q.14, C:D.15, C:D.15, C:N.41, C:D.66, C:L.67, C:L.88, C:A.90, C:S.92, C:Y.103, C:Y.159, C:K.163, C:H.189, C:H.189, C:R.194, C:R.194, B:S.38, B:S.38 Water bridges: C:I.11, C:G.16, C:R.35, C:G.195, B:S.38, B:S.39 Salt bridges: C:R.35, B:R.36 pi-Cation interactions: C:R.35 NAP.18: 30 residues within 4Å: Chain A: R.36, S.37, S.38 Chain D: G.10, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, L.88, G.89, A.90, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163, L.186, F.187, N.188, H.189, R.194 Ligands: EDO.6, F7E.17 33 PLIP interactions: 28 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:L.186 Hydrogen bonds: D:G.10, D:T.12, D:T.12, D:T.12, D:G.13, D:Q.14, D:Q.14, D:D.15, D:D.15, D:N.41, D:D.66, D:L.67, D:L.88, D:A.90, D:S.92, D:Y.159, D:K.163, D:H.189, D:H.189, D:R.194, D:R.194, A:S.38, A:S.38 Water bridges: D:I.11, D:G.16, D:R.35, D:G.195, A:S.38, A:S.39 Salt bridges: D:R.35, A:R.36 pi-Cation interactions: D:R.35

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

EDO.4: 3 residues within 4Å: Chain A: R.156, P.306 Chain B: E.175 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:E.175 Hydrogen bonds: A:R.156, A:R.156, A:P.306 EDO.5: 4 residues within 4Å: Chain A: R.174, E.175 Chain B: Y.154 Ligands: EDO.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.174, B:Y.154 EDO.6: 8 residues within 4Å: Chain A: R.35, S.37, N.41 Chain D: R.35, S.37, N.41 Ligands: NAP.3, NAP.18 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.35, D:S.37, D:N.41, A:R.35, A:N.41 EDO.7: 6 residues within 4Å: Chain A: Y.167, W.168, R.174, D.250 Chain B: Y.154 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.167, A:Y.167 EDO.10: 6 residues within 4Å: Chain A: Y.154 Chain B: Y.167, W.168, R.174, D.250 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.167 Water bridges: B:D.250 EDO.11: 4 residues within 4Å: Chain A: Y.154 Chain B: R.174, E.175 Ligands: EDO.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.174, A:Y.154 EDO.14: 8 residues within 4Å: Chain B: R.35, S.37, N.41 Chain C: R.35, S.37, N.41 Ligands: NAP.9, NAP.13 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.35, C:S.37, C:N.41, B:S.37, B:N.41 EDO.15: 6 residues within 4Å: Chain C: Y.167, W.168, V.171, R.174, D.250 Chain D: Y.154 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.167, C:R.174, C:D.250, C:D.250 Water bridges: C:E.175 EDO.16: 6 residues within 4Å: Chain C: Y.154 Chain D: Y.167, W.168, V.171, R.174, D.250 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.250 Water bridges: D:Y.167, D:Y.167, D:D.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pfeiffer, M. et al., A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase. Acs Catalysis (2019)

Release Date

2018-07-18

Peptides

GDP-mannose 4,6 dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

GDP-mannose 4,6 dehydratase

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