SMTL ID : 2c5a.1

GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x GDC: GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE(Non-covalent)

GDC.1: 28 residues within 4Å: Chain A: M.104, G.105, G.106, M.107, I.110, S.145, A.146, C.147, F.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: NAD.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.105, A:M.107, A:S.145, A:F.203, A:N.205, A:N.205, A:E.218, A:A.220, A:W.238, A:Q.243, A:P.302, A:R.308, A:S.358, A:S.358 Water bridges: A:R.308 Salt bridges: A:R.245, A:R.308, A:R.308 pi-Stacking: A:F.224, A:W.238 GDC.15: 28 residues within 4Å: Chain B: M.104, G.105, G.106, M.107, I.110, S.145, A.146, C.147, F.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: NAD.16 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.105, B:M.107, B:S.145, B:F.203, B:N.205, B:N.205, B:E.218, B:A.220, B:W.238, B:Q.243, B:P.302, B:R.308, B:S.358, B:S.358 Water bridges: B:G.108, B:R.308 Salt bridges: B:K.219, B:K.219, 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.2: 28 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, F.176, K.180, F.203, N.205, I.206, K.219 Ligands: GDC.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.203 Hydrogen bonds: A:G.39, 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:K.180, A:I.206, A:I.206, A:K.219 Water bridges: A:G.39, A:A.42, A:T.212, A:T.212, A:T.212, A:T.212, A:K.219 pi-Stacking: A:W.61, A:W.61, A:F.203 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, F.176, K.180, F.203, N.205, I.206, K.219, R.373 Ligands: GDC.15 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.203 Hydrogen bonds: B:G.38, 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:K.180, B:I.206, B:I.206, B:K.219, B:R.373 Water bridges: B:A.42, B:T.212, B:T.212, B:T.212, B:T.212, B:R.373 pi-Stacking: B:W.61, B:W.61, B:F.203

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

FMT.3: 4 residues within 4Å: Chain A: T.15, Y.16, K.17, E.18 Ligand excluded by PLIP 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: 2 residues within 4Å: Chain A: G.362, T.363 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: R.21, R.48, D.251, V.254 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: T.212, W.213, K.214 Ligand excluded by PLIP FMT.8: 2 residues within 4Å: Chain A: E.164, S.165 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: N.191, K.192, R.266 Ligand excluded by PLIP FMT.10: 2 residues within 4Å: Chain A: T.158, N.159 Ligand excluded by PLIP FMT.11: 3 residues within 4Å: Chain A: R.259, G.320, W.321 Ligand excluded by PLIP FMT.12: 6 residues within 4Å: Chain A: D.103, V.116, N.120, R.217, Q.364, R.373 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain A: N.64, E.65, H.66, M.67, G.377 Ligand excluded by PLIP FMT.14: 7 residues within 4Å: Chain A: K.214, G.215, R.226, L.354, Y.355, S.357, K.359 Ligand excluded by PLIP FMT.17: 2 residues within 4Å: Chain B: D.274, N.309 Ligand excluded by PLIP FMT.18: 5 residues within 4Å: Chain B: L.19, R.21, R.48, D.251, V.254 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain B: V.79, D.80, N.86, G.370, S.371, L.372 Ligand excluded by PLIP FMT.20: 2 residues within 4Å: Chain B: E.164, S.165 Ligand excluded by PLIP FMT.21: 7 residues within 4Å: Chain B: K.214, G.215, R.226, L.354, Y.355, S.357, K.359 Ligand excluded by PLIP

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.22: 6 residues within 4Å: Chain A: E.171, P.172, Q.173 Chain B: W.168, E.185, K.188 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.171, A:E.171, A:P.172, B:K.188, B:K.188 Water bridges: A:E.151, A:E.151, A:P.172, A:Q.173 Salt bridges: B:E.185

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