SMTL ID : 6gpj.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 4 residues within 4Å: Chain A: N.197, K.202, Y.303 Chain D: Y.64 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.197, D:Y.64 Salt bridges: A:K.202, A:K.302 CIT.10: 4 residues within 4Å: Chain A: Y.64 Chain D: N.197, K.202, Y.303 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.303 Hydrogen bonds: D:N.197 Water bridges: D:K.202, D:K.202, D:K.302 Salt bridges: D:K.202, D:K.302

4 x G4F: [[(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},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate(Non-covalent)

G4F.2: 25 residues within 4Å: Chain A: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, 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, L.312 Ligands: NAP.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.135, A:S.136, A:E.137, 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:R.305, A:V.309 Water bridges: A:S.92, A:N.197, A:K.202, A:R.227, A:R.227, A:R.305 Salt bridges: A:R.194, A:R.227, A:R.305, A:R.305 G4F.5: 25 residues within 4Å: Chain B: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, 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, L.312 Ligands: NAP.6 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:S.136, B:E.137, B:E.137, B:Y.159, B:N.188, B:R.194, B:R.194, B:N.197, B:N.197, B:V.199, B:K.202, B:G.221, B:N.222, B:R.305, B:R.305, B:V.309 Water bridges: B:S.92, B:R.227, B:R.227, B:R.305 Salt bridges: B:R.194, B:R.227, B:R.305, B:R.305 Halogen bonds: B:T.135 G4F.7: 24 residues within 4Å: Chain C: S.92, V.94, T.135, S.136, E.137, Y.159, 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, L.312 Ligands: NAP.8 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:T.135, C:S.136, C:E.137, C:E.137, C:Y.159, 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:R.305, C:V.309 Water bridges: C:N.197, C:K.202, C:R.227, C:R.305, C:R.305 Salt bridges: C:R.194, C:R.227, C:R.305, C:R.305 G4F.11: 25 residues within 4Å: Chain D: S.92, H.93, V.94, T.135, S.136, E.137, Y.159, 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, L.312 Ligands: NAP.12 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:S.136, D:E.137, D:Y.159, 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:R.305, D:V.309 Water bridges: D:S.92, D:N.197, D:K.202, D:R.227, D:R.305, D:R.305 Salt bridges: D:R.194, D:R.227, D:R.305, D:R.305 Halogen bonds: D:T.135

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

NAP.3: 30 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, Q.91, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163, L.186, N.188, H.189, R.194 Chain D: R.36, S.37, S.38 Ligands: G4F.2 33 PLIP interactions: 29 interactions with chain A, 4 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:I.11, A:D.15, A:G.16, A:R.35, A:R.35, A:G.195, D:R.36, D:S.38 Salt bridges: A:R.35, D:R.36 pi-Cation interactions: A:R.35 NAP.6: 30 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: G4F.5 33 PLIP interactions: 29 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.10, B:T.12, 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:Y.159, B:K.163, B:H.189, B:H.189, B:R.194, B:R.194, C:S.38 Water bridges: B:G.10, B:I.11, B:G.16, B:R.35, 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.8: 29 residues within 4Å: Chain B: R.36, S.37, S.38 Chain C: G.10, T.12, G.13, Q.14, D.15, R.35, D.66, L.67, L.88, G.89, A.90, Q.91, 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: G4F.7 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain B 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:N.41, C:D.66, C:L.67, C:L.88, C:A.90, C:S.92, C:Y.103, C:K.163, C:H.189, C:H.189, C:R.194, C:R.194, B:S.38 Water bridges: C:G.10, C:G.10, C:I.11, C:G.16, C:R.35, C:R.35, C:G.195, B:R.36, B:S.38, B:S.39 Salt bridges: C:R.35, B:R.36 pi-Cation interactions: C:R.35 NAP.12: 29 residues within 4Å: Chain A: R.36, S.37, S.38 Chain D: 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, N.188, H.189, R.194 Ligands: G4F.11 34 PLIP interactions: 30 interactions with chain D, 4 interactions with chain A 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: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 Water bridges: D:G.10, D:G.10, D:G.10, D:D.15, D:G.16, D:R.35, D:Y.103, D:G.195, A:S.38, A:S.39 Salt bridges: D:R.35, A:R.36 pi-Cation interactions: D:R.35

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

EDO.4: 5 residues within 4Å: Chain B: Y.167, W.168, R.174, D.250 Chain D: Y.154 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.167, D:Y.154 Water bridges: B:D.250, B:D.250 EDO.9: 5 residues within 4Å: Chain D: S.37, S.38, S.39, F.40, N.41 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:S.38, D:N.41, D:N.41 Water bridges: D:S.37, D:S.37, A:A.196, A:N.197, A:N.197

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
A

B
D

C
C

D
B

GDP-mannose 4,6 dehydratase

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