SMTL ID : 6gpk.1

Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: F.174, L.185, W.189 Chain D: F.174, L.185, W.189 Ligands: EDO.7 Ligand excluded by PLIP EDO.2: 8 residues within 4Å: Chain A: R.56, S.58, N.62 Chain B: R.56, S.58, N.62 Ligands: NAP.14, NAP.23 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: R.283, W.299, E.300, G.301, E.306 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.135 Chain C: T.89 Chain D: E.123, Y.124, D.127 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: Y.188, W.189, R.195, D.271 Chain D: Y.175 Ligands: EDO.11 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: T.89 Chain B: E.123, Y.124, D.127 Chain C: R.135 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: E.170, T.171, T.172, P.173, F.174, W.189 Ligands: EDO.1 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: R.177 Chain D: E.196 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: T.276, E.278, P.348, R.349, V.350, A.351 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: H.292, H.361, V.364 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: V.192, R.195, E.196 Chain D: Y.175 Ligands: EDO.5 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: E.165, P.173 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: F.119, D.120, L.121, A.122, E.123 Chain B: D.90, T.92, C.93 Chain D: D.138 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: D.138, F.194, Y.198 Chain C: F.119, A.122, P.179 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.123, D.127 Chain B: T.89 Chain D: R.135 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: F.174, L.185, W.189 Chain C: F.174, L.185, W.189 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: R.135 Chain C: E.123, D.127 Chain D: T.89 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: V.192, R.195, E.196 Chain C: Y.175 Ligands: EDO.22 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain B: L.83, Y.85 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: Y.188, W.189, R.195, D.271 Chain C: Y.175 Ligands: EDO.20 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: R.283, W.299, E.300, G.301, E.306 Ligands: GOL.30 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain C: Q.342, N.345 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: R.56, S.58, N.62 Chain D: R.56, S.58, N.62 Ligands: NAP.31, NAP.36 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: Y.175 Chain C: V.192, R.195, E.196 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: Y.175 Chain C: Y.188, W.189, R.195, D.271 Ligands: EDO.28 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain D: E.165, K.169, T.171, T.172 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain A: Y.175 Chain D: V.192, R.195, E.196 Ligands: EDO.35 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: Y.188, W.189, R.195, D.271 Ligands: EDO.34 Ligand excluded by PLIP

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

NAP.14: 31 residues within 4Å: Chain A: G.31, I.32, T.33, G.34, Q.35, D.36, R.56, N.62, D.87, L.88, L.109, G.110, A.111, S.113, Y.124, V.128, A.154, S.155, T.156, Y.180, K.184, L.207, F.208, N.209, H.210, R.215 Chain B: R.57, S.58, S.59 Ligands: EDO.2, GDD.15 33 PLIP interactions: 28 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.207 Hydrogen bonds: A:G.31, A:T.33, A:T.33, A:G.34, A:Q.35, A:Q.35, A:D.36, A:N.62, A:D.87, A:L.88, A:L.109, A:A.111, A:S.113, A:Y.180, A:K.184, A:H.210, A:H.210, A:R.215, A:R.215, B:S.59, B:S.59 Water bridges: A:G.31, A:I.32, A:G.37, A:R.56, A:R.56, A:G.216, B:S.59, B:S.60 Salt bridges: A:R.56, B:R.57 pi-Cation interactions: A:R.56 NAP.23: 31 residues within 4Å: Chain A: R.57, S.58, S.59 Chain B: G.31, I.32, T.33, G.34, Q.35, D.36, R.56, N.62, D.87, L.88, L.109, G.110, A.111, S.113, Y.124, V.128, A.154, S.155, T.156, Y.180, K.184, L.207, F.208, N.209, H.210, R.215 Ligands: EDO.2, GDD.24 33 PLIP interactions: 28 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.207 Hydrogen bonds: B:G.31, B:T.33, B:T.33, B:T.33, B:G.34, B:Q.35, B:Q.35, B:D.36, B:N.62, B:D.87, B:L.88, B:L.109, B:A.111, B:S.113, B:Y.124, B:K.184, B:H.210, B:H.210, B:R.215, B:R.215, A:S.59 Water bridges: B:G.31, B:I.32, B:G.37, B:R.56, B:G.216, A:R.57, A:S.59, A:S.60 Salt bridges: B:R.56, A:R.57 pi-Cation interactions: B:R.56 NAP.31: 30 residues within 4Å: Chain C: G.31, T.33, G.34, Q.35, D.36, R.56, N.62, D.87, L.88, L.109, G.110, A.111, S.113, Y.124, V.128, A.154, S.155, T.156, Y.180, K.184, L.207, F.208, N.209, H.210, R.215 Chain D: R.57, S.58, S.59 Ligands: EDO.27, GDD.32 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.31, C:T.33, C:T.33, C:T.33, C:G.34, C:Q.35, C:Q.35, C:D.36, C:N.62, C:D.87, C:L.88, C:L.109, C:A.111, C:S.113, C:Y.124, C:K.184, C:H.210, C:H.210, C:R.215, C:R.215, D:S.59, D:S.59 Water bridges: C:G.31, C:I.32, C:D.36, C:G.37, C:R.56, C:R.56, C:G.216, D:S.59, D:S.60 Salt bridges: C:R.56, D:R.57 pi-Cation interactions: C:R.56 NAP.36: 31 residues within 4Å: Chain C: R.57, S.58, S.59 Chain D: G.31, I.32, T.33, G.34, Q.35, D.36, R.56, N.62, D.87, L.88, L.109, G.110, A.111, S.113, Y.124, V.128, A.154, S.155, T.156, Y.180, K.184, L.207, F.208, N.209, H.210, R.215 Ligands: EDO.27, GDD.37 31 PLIP interactions: 27 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.31, D:T.33, D:T.33, D:T.33, D:G.34, D:Q.35, D:Q.35, D:D.36, D:D.36, D:N.62, D:D.87, D:L.88, D:L.109, D:A.111, D:S.113, D:Y.180, D:K.184, D:H.210, D:H.210, D:R.215, D:R.215, C:S.59 Water bridges: D:I.32, D:G.37, D:R.56, D:R.65, C:R.57, C:S.60 Salt bridges: D:R.56, C:R.57 pi-Cation interactions: D:R.56

4 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)

GDD.15: 25 residues within 4Å: Chain A: S.113, H.114, V.115, T.156, S.157, Q.158, Y.180, N.209, R.215, N.218, F.219, V.220, K.223, L.241, G.242, N.243, A.246, R.248, V.282, Y.324, R.326, E.329, V.330, L.333 Ligands: NAP.14 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.113, A:T.156, A:T.156, A:S.157, A:Q.158, A:Q.158, A:N.209, A:R.215, A:R.215, A:N.218, A:V.220, A:K.223, A:G.242, A:N.243, A:R.326, A:E.329 Water bridges: A:S.113, A:N.218, A:K.223, A:R.248, A:R.248, A:Y.324, A:R.326, A:E.329 Salt bridges: A:R.248, A:R.326, A:R.326 GDD.24: 25 residues within 4Å: Chain B: S.113, H.114, V.115, T.156, S.157, Q.158, Y.180, N.209, R.215, N.218, F.219, V.220, K.223, L.241, G.242, N.243, A.246, R.248, V.282, Y.324, R.326, E.329, V.330, L.333 Ligands: NAP.23 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:S.113, B:T.156, B:S.157, B:Q.158, B:Q.158, B:Y.180, B:N.209, B:R.215, B:R.215, B:N.218, B:V.220, B:K.223, B:G.242, B:N.243, B:R.326, B:E.329 Water bridges: B:S.113, B:N.218, B:N.218, B:K.223, B:R.248, B:R.248, B:Y.324, B:E.329 Salt bridges: B:R.248, B:R.326, B:R.326 GDD.32: 24 residues within 4Å: Chain C: S.113, H.114, V.115, T.156, S.157, Q.158, Y.180, N.209, R.215, N.218, F.219, V.220, K.223, L.241, G.242, N.243, A.246, R.248, V.282, Y.324, R.326, E.329, L.333 Ligands: NAP.31 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:S.113, C:T.156, C:S.157, C:Q.158, C:Q.158, C:Y.180, C:N.209, C:R.215, C:R.215, C:N.218, C:V.220, C:K.223, C:G.242, C:N.243, C:R.326, C:E.329 Water bridges: C:S.113, C:N.218, C:N.218, C:K.223, C:R.248, C:Y.324, C:R.326 Salt bridges: C:R.248, C:R.326, C:R.326 GDD.37: 24 residues within 4Å: Chain D: S.113, H.114, V.115, T.156, S.157, Q.158, Y.180, N.209, R.215, N.218, F.219, V.220, K.223, L.241, G.242, N.243, A.246, R.248, V.282, Y.324, R.326, E.329, L.333 Ligands: NAP.36 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:S.113, D:T.156, D:T.156, D:S.157, D:Q.158, D:Q.158, D:N.209, D:R.215, D:R.215, D:N.218, D:V.220, D:K.223, D:G.242, D:N.243, D:R.326, D:E.329 Water bridges: D:S.113, D:N.218, D:N.218, D:K.223, D:R.248, D:R.248, D:R.326 Salt bridges: D:R.248, D:R.326, D:R.326

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 4 residues within 4Å: Chain C: D.245, R.283, W.299 Ligands: EDO.25 No protein-ligand interaction detected (PLIP)

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
B

C
C

D
D

GDP-mannose 4,6 dehydratase