SMTL ID : 2c54.1

gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x GKE: GUANOSINE 5'-DIPHOSPHATE-BETA-L-GULOSE(Non-covalent)

GKE.1: 27 residues within 4Å: Chain A: G.105, G.106, M.107, I.110, S.145, C.147, Y.176, F.203, H.204, N.205, E.218, K.219, A.220, A.223, F.224, K.227, M.237, W.238, Q.243, R.245, M.279, P.302, E.303, R.308, S.358 Ligands: GKD.2, NAD.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:M.107, A:S.145, A:C.147, A:N.205, A:N.205, A:E.218, A:A.220, A:W.238, A:Q.243, A:E.303, A:R.308, A:S.358 Water bridges: A:G.108, A:R.245 Salt bridges: A:R.245, A:R.308, A:R.308 pi-Stacking: A:F.224, A:W.238 GKE.14: 27 residues within 4Å: Chain B: G.105, G.106, M.107, I.110, S.145, C.147, Y.176, F.203, H.204, N.205, E.218, K.219, A.220, A.223, F.224, K.227, M.237, W.238, Q.243, R.245, M.279, P.302, E.303, R.308, S.358 Ligands: GKD.15, NAD.16 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:M.107, B:S.145, B:C.147, B:N.205, B:N.205, B:E.218, B:A.220, B:W.238, B:Q.243, B:E.303, B:R.308, B:S.358 Water bridges: B:G.106, B:R.308 Salt bridges: B:R.245, B:R.308, B:R.308 pi-Stacking: B:F.224, B:W.238

2 x GKD: GUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE(Non-covalent)

GKD.2: 28 residues within 4Å: Chain A: G.105, G.106, M.107, I.110, S.145, A.146, C.147, Y.176, F.203, H.204, N.205, E.218, K.219, A.220, A.223, F.224, K.227, M.237, W.238, Q.243, R.245, M.279, P.302, E.303, R.308, S.358 Ligands: GKE.1, NAD.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:M.107, A:S.145, A:Y.176, A:N.205, A:N.205, A:E.218, A:A.220, A:W.238, A:Q.243, A:E.303, A:R.308, A:S.358 Water bridges: A:G.108, A:R.245 Salt bridges: A:R.245, A:R.308, A:R.308 pi-Stacking: A:F.224, A:W.238 GKD.15: 28 residues within 4Å: Chain B: G.105, G.106, M.107, I.110, S.145, A.146, C.147, Y.176, F.203, H.204, N.205, E.218, K.219, A.220, A.223, F.224, K.227, M.237, W.238, Q.243, R.245, M.279, P.302, E.303, R.308, S.358 Ligands: GKE.14, NAD.16 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:M.107, B:S.145, B:Y.176, B:N.205, B:N.205, B:E.218, B:A.220, B:W.238, B:Q.243, B:E.303, B:R.308, B:S.358 Water bridges: B:G.106, B:R.245, B:R.308 Salt bridges: B:R.245, B:R.308, B:R.308 pi-Stacking: B:F.224, B:W.238

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 29 residues within 4Å: Chain A: G.36, G.38, G.39, F.40, I.41, D.60, W.61, K.62, V.79, D.80, L.81, R.82, L.100, A.101, A.102, D.103, M.104, I.124, A.143, S.144, S.145, Y.176, R.180, F.203, N.205, I.206, K.219 Ligands: GKE.1, GKD.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.203 Hydrogen bonds: A:G.38, A:F.40, A:I.41, A:W.61, A:D.80, A:L.81, A:R.82, A:L.100, A:A.102, A:R.180, A:I.206, A:I.206, A:K.219 Water bridges: A:A.42, A:K.62, A:R.180, A:T.212, A:T.212, A:T.212, A:T.212 pi-Stacking: A:W.61, A:W.61 NAD.16: 29 residues within 4Å: Chain B: G.36, G.38, G.39, F.40, I.41, D.60, W.61, K.62, V.79, D.80, L.81, R.82, L.100, A.101, A.102, D.103, M.104, I.124, A.143, S.144, S.145, Y.176, R.180, F.203, N.205, I.206, K.219 Ligands: GKE.14, GKD.15 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:F.203 Hydrogen bonds: B:G.36, B:F.40, B:I.41, B:W.61, B:D.80, B:D.80, B:L.81, B:R.82, B:L.100, B:A.102, B:R.180, B:I.206, B:I.206 Water bridges: B:A.42, B:R.180, B:T.212, B:T.212, B:T.212, B:T.212, B:T.212, B:K.219, B:K.219, B:R.373 Salt bridges: B:K.219 pi-Stacking: B:W.61, B:W.61

18 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 6 residues within 4Å: Chain A: V.79, D.80, N.86, G.370, S.371, L.372 Ligand excluded by PLIP FMT.5: 6 residues within 4Å: Chain A: K.214, G.215, R.226, L.354, Y.355, S.357 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: T.15, Y.16, K.17, E.18 Ligand excluded by PLIP FMT.7: 4 residues within 4Å: Chain A: Q.368, L.369 Chain B: M.84, I.134 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: R.21, R.48, D.251, V.254 Ligand excluded by PLIP FMT.9: 1 residues within 4Å: Chain A: N.159 Ligand excluded by PLIP FMT.10: 2 residues within 4Å: Chain A: R.217, Q.364 Ligand excluded by PLIP FMT.11: 2 residues within 4Å: Chain A: F.152 Chain B: P.169 Ligand excluded by PLIP FMT.12: 2 residues within 4Å: Chain A: E.164, S.165 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain B: T.212, W.213, K.214 Ligand excluded by PLIP FMT.18: 7 residues within 4Å: Chain B: K.214, G.215, R.226, L.354, Y.355, S.357, K.359 Ligand excluded by PLIP FMT.19: 3 residues within 4Å: Chain B: Q.111, S.112, H.114 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain B: Y.24, W.25, P.26, K.262 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain B: R.217, V.361, Q.364, R.373 Ligand excluded by PLIP FMT.22: 2 residues within 4Å: Chain B: E.69, D.70 Ligand excluded by PLIP FMT.23: 6 residues within 4Å: Chain B: L.19, R.21, R.48, D.251, V.254, E.255 Ligand excluded by PLIP FMT.24: 2 residues within 4Å: Chain B: K.50, H.51 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain B: S.231, T.232, D.233, R.234 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 9 residues within 4Å: Chain A: E.164, S.165, W.168, E.185, K.188 Chain B: E.171, P.172, D.174, L.178 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.174 Water bridges: B:E.171, A:E.164, A:W.168, A:W.168, A:E.185, A:K.188 Salt bridges: B:E.171, B:E.171, A:E.185, A:E.185 pi-Cation interactions: A:W.168, A:W.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Major, L.L. et al., Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site. J. Am. Chem. Soc. (2005)

Release Date

2005-11-14

Peptides

GDP-MANNOSE-3', 5'-EPIMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP-MANNOSE-3', 5'-EPIMERASE