SMTL ID : 1t2a.1

Crystal structure of human GDP-D-mannose 4,6-dehydratase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: G.31, I.32, T.33, G.34, Q.35, D.36, R.56, 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, N.209, H.210, R.215 Chain D: R.57, S.58, S.59 33 PLIP interactions: 29 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:G.31, A:T.33, 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.124, A:K.184, A:H.210, A:H.210, A:R.215, A:R.215, D:S.59, D:S.59, D:S.59 Water bridges: A:G.31, A:G.31, A:G.37, A:R.56, A:R.56, A:R.56, A:G.216 Salt bridges: A:R.56, D:R.57 pi-Cation interactions: A:R.56 NDP.3: 30 residues within 4Å: Chain B: G.31, I.32, T.33, G.34, Q.35, D.36, R.56, D.87, L.88, L.109, G.110, A.111, Q.112, S.113, Y.124, V.128, A.154, S.155, T.156, Y.180, K.184, L.207, F.208, N.209, H.210, E.211, R.215 Chain C: R.57, S.58, S.59 35 PLIP interactions: 31 interactions with chain B, 4 interactions with chain C 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: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, C:S.59 Water bridges: B:G.31, B:G.31, B:G.31, B:G.37, B:R.56, B:R.56, B:R.56, B:N.62, B:G.216, C:S.59, C:S.60 Salt bridges: B:R.56, C:R.57 pi-Cation interactions: B:R.56 NDP.5: 29 residues within 4Å: Chain B: R.57, S.58, S.59 Chain C: 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 35 PLIP interactions: 4 interactions with chain B, 31 interactions with chain C Hydrogen bonds: B:S.59, 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:D.36, C:N.62, C:D.87, C:L.88, C:L.109, C:A.111, C:S.113, C:Y.124, C:Y.180, C:K.184, C:H.210, C:H.210, C:R.215, C:R.215 Water bridges: B:S.59, B:S.60, C:I.32, C:G.37, C:R.56, C:R.56, C:R.56, C:G.216 Salt bridges: B:R.57, C:R.56 Hydrophobic interactions: C:L.207 pi-Cation interactions: C:R.56 NDP.7: 30 residues within 4Å: Chain A: R.57, S.58, S.59 Chain D: G.31, I.32, T.33, G.34, Q.35, D.36, R.56, D.87, L.88, L.109, G.110, A.111, Q.112, S.113, Y.124, V.128, A.154, S.155, T.156, Y.180, K.184, L.207, F.208, N.209, H.210, E.211, R.215 34 PLIP interactions: 31 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.207 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: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, A:S.59 Water bridges: D:G.31, D:G.37, D:R.56, D:N.62, D:N.62, D:N.62, D:N.62, D:R.65, D:R.215, A:S.60 Salt bridges: D:R.56, A:R.57 pi-Cation interactions: D:R.56

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

GDP.2: 17 residues within 4Å: Chain A: H.114, V.115, E.158, N.209, 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 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:H.114, A:E.158, A:N.209, A:N.218, A:V.220, A:K.223, A:G.242, A:R.326, A:R.326 Water bridges: A:E.158, A:R.215, A:R.215, A:R.215, A:N.218, A:N.218, A:N.218, A:K.223, A:N.243, A:R.248, A:R.326 Salt bridges: A:R.248, A:R.326, A:R.326 GDP.4: 18 residues within 4Å: Chain B: H.114, V.115, E.158, N.209, 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 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:E.158, B:N.209, B:N.218, B:V.220, B:K.223, B:G.242, B:N.243, B:R.248, B:R.326, B:R.326, B:V.330 Water bridges: B:E.158, B:R.215, B:R.215, B:R.215, B:N.218, B:N.218, B:R.326 Salt bridges: B:R.248, B:R.326, B:R.326 GDP.6: 17 residues within 4Å: Chain C: H.114, V.115, E.158, N.209, 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 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:E.158, C:N.209, C:N.218, C:V.220, C:K.223, C:G.242, C:R.326, C:R.326, C:V.330 Water bridges: C:H.114, C:E.158, C:E.158, C:R.215, C:R.215, C:R.215, C:N.218, C:K.223, C:N.243, C:R.248, C:R.326 Salt bridges: C:R.248, C:R.326, C:R.326 GDP.8: 18 residues within 4Å: Chain D: H.114, V.115, E.158, N.209, 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 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:H.114, D:E.158, D:N.209, D:N.218, D:V.220, D:K.223, D:G.242, D:N.243, D:R.326, D:R.326, D:V.330 Water bridges: D:E.158, D:E.158, D:E.158, D:E.158, D:R.215, D:R.215, D:R.215, D:N.218, D:K.223, D:R.248 Salt bridges: D:R.248, D:R.326, D:R.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vedadi, M. et al., Crystal Structure and Biophysical Characterization of Human GDP-D-mannose 4,6-dehydratase. To be Published

Release Date

2004-05-10

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