SMTL ID : 2c59.1

gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), with gdp-alpha-d-mannose and gdp-beta-l-galactose bound in the active site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

GDD.1: 29 residues within 4Å: Chain A: M.104, 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: GDC.2, NAD.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:M.107, A:S.145, A:C.147, 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, A:S.358 Water bridges: A:G.108, A:R.245, A:R.245 Salt bridges: A:R.245, A:R.308 pi-Stacking: A:F.224, A:W.238, A:W.238 GDD.13: 29 residues within 4Å: Chain B: M.104, 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: GDC.14, NAD.15 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:M.107, B:S.145, 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:S.358, B:S.358 Water bridges: B:G.108, B:R.245, B:R.308, B:R.308 Salt bridges: B:R.245, B:R.308, B:R.308 pi-Stacking: B:F.224, B:W.238

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

GDC.2: 28 residues within 4Å: Chain A: M.104, 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: GDD.1, NAD.3 22 PLIP interactions: 22 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:P.302, A:S.358, A:S.358 Water bridges: A:G.108, A:R.245, A:R.245, A:R.308, A:R.308 Salt bridges: A:R.245, A:R.308 pi-Stacking: A:F.224, A:W.238, A:W.238 GDC.14: 29 residues within 4Å: Chain B: M.104, 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: GDD.13, NAD.15 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:M.107, B:S.145, B:Y.176, B:Y.176, B:N.205, 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:R.245, 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, K.180, F.203, N.205, I.206, K.219 Ligands: GDD.1, GDC.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.203 Hydrogen bonds: A:G.36, 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:A.42, A:K.62, A:T.212, A:T.212, A:T.212 pi-Stacking: A:W.61, A:W.61, A:F.203 NAD.15: 29 residues within 4Å: Chain B: G.36, G.38, G.39, F.40, I.41, D.60, W.61, 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, K.180, F.203, N.205, I.206, K.219, R.373 Ligands: GDD.13, GDC.14 22 PLIP interactions: 22 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 pi-Stacking: B:W.61, B:W.61, B:F.203

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

FMT.4: 8 residues within 4Å: Chain A: K.214, G.215, G.216, R.226, L.354, Y.355, S.357, K.359 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.215, A:G.216 Water bridges: A:R.226, A:K.359, A:K.359 FMT.5: 2 residues within 4Å: Chain A: F.152 Chain B: P.169 No protein-ligand interaction detected (PLIP) FMT.6: 4 residues within 4Å: Chain A: E.20, R.259, G.320, W.321 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.259, A:R.259 Water bridges: A:G.320, A:A.322 FMT.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.8: 2 residues within 4Å: Chain B: R.217, Q.364 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.217, B:Q.364 Water bridges: B:R.217, B:R.373 FMT.9: 4 residues within 4Å: Chain B: S.231, T.232, D.233, R.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.232, B:D.233, B:R.234 FMT.10: 6 residues within 4Å: Chain A: V.79, D.80, N.86, G.370, S.371, L.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.80, A:N.86 FMT.11: 2 residues within 4Å: Chain A: P.169 Chain B: F.152 No protein-ligand interaction detected (PLIP)

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

BTB.12: 8 residues within 4Å: Chain B: K.31, Y.55, I.57, E.75, K.89, V.90, E.92, G.93 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.31, B:Y.55, B:Y.55, B:K.89, B:E.92, B:E.92 Salt bridges: B:E.75

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