SMTL ID : 1e7q.1

GDP 4-keto-6-deoxy-D-mannose epimerase reductase S107A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 25 residues within 4Å: Chain A: G.10, R.12, G.13, M.14, V.15, R.36, L.39, N.40, L.41, L.42, A.62, A.63, A.64, V.66, I.86, L.105, G.106, A.107, S.108, Y.136, K.140, P.163, T.164, N.165, L.166 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:P.163, A:L.166 Hydrogen bonds: A:M.14, A:V.15, A:N.40, A:L.41, A:L.42, A:A.64, A:S.108, A:Y.136, A:Y.136, A:K.140, A:L.166 Water bridges: A:G.10, A:R.12, A:G.16, A:R.36, A:R.36, A:R.36, A:R.36, A:V.66, A:L.166 Salt bridges: A:R.36 NAP.8: 25 residues within 4Å: Chain B: G.10, R.12, G.13, M.14, V.15, R.36, L.39, N.40, L.41, L.42, A.62, A.63, A.64, V.66, I.86, L.105, G.106, A.107, S.108, Y.136, K.140, P.163, T.164, N.165, L.166 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.163, B:L.166 Hydrogen bonds: B:M.14, B:V.15, B:N.40, B:L.41, B:L.42, B:A.64, B:S.108, B:Y.136, B:Y.136, B:K.140, B:L.166 Water bridges: B:G.10, B:R.12, B:G.16, B:R.36, B:R.36, B:R.36, B:R.36, B:V.66, B:L.166 Salt bridges: B:R.36

2 x UVW: ACETYLPHOSPHATE(Non-covalent)

UVW.2: 7 residues within 4Å: Chain A: G.67, G.68, I.69, V.70, A.71, N.177, S.178 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.71 Hydrogen bonds: A:G.68, A:I.69, A:V.70, A:S.178, A:S.178 Water bridges: A:A.71, A:A.71 UVW.9: 7 residues within 4Å: Chain B: G.67, G.68, I.69, V.70, A.71, N.177, S.178 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.71 Hydrogen bonds: B:G.68, B:I.69, B:V.70, B:S.178, B:S.178 Water bridges: B:A.71, B:A.71

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.5, V.32, R.34, E.54 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.33 Salt bridges: A:R.5, A:R.34 SO4.4: 4 residues within 4Å: Chain A: H.11, R.12, R.20, T.35 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.11, A:R.20 Salt bridges: A:H.11, A:R.12, A:R.20 SO4.5: 3 residues within 4Å: Chain A: D.198, R.269, V.271 No protein-ligand interaction detected (PLIP) SO4.6: 3 residues within 4Å: Chain A: R.152, P.238, M.239 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.152, A:R.152 Salt bridges: A:R.152 SO4.10: 4 residues within 4Å: Chain B: R.5, V.32, R.34, E.54 3 PLIP interactions: 3 interactions with chain B Water bridges: B:L.33 Salt bridges: B:R.5, B:R.34 SO4.11: 4 residues within 4Å: Chain B: H.11, R.12, R.20, T.35 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.11, B:R.20 Salt bridges: B:H.11, B:R.12, B:R.20 SO4.12: 3 residues within 4Å: Chain B: D.198, R.269, V.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.198 SO4.13: 3 residues within 4Å: Chain B: R.152, P.238, M.239 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.152, B:R.152 Salt bridges: B:R.152

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 4 residues within 4Å: Chain A: S.17, R.21, H.170, W.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21 Water bridges: A:H.170 TRS.14: 4 residues within 4Å: Chain B: S.17, R.21, H.170, W.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.21 Water bridges: B:H.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosano, C. et al., Probing the Catalytic Mechanism of Gdp-4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase by Kinetic and Crystallographic Characterization of Site-Specific Mutants. J.Mol.Biol. (2000)

Release Date

2000-10-18

Peptides

GDP-FUCOSE SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GDP-FUCOSE SYNTHETASE