SMTL ID : 1e7r.1

GDP 4-keto-6-deoxy-D-mannose epimerase reductase Y136E

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: 21 residues within 4Å: Chain A: G.10, 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, S.107, K.140, P.163, T.164, L.166 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.163, A:L.166, A:L.166 Hydrogen bonds: A:M.14, A:V.15, A:N.40, A:L.41, A:L.42, A:A.64, A:L.166, A:L.166 Water bridges: A:G.10, A:G.13, A:G.16, A:R.36, A:R.36, A:R.36, A:R.36, A:A.63, A:L.105, A:S.107, A:E.136, A:K.140, A:H.170, A:H.179 Salt bridges: A:R.36 NAP.7: 21 residues within 4Å: Chain B: G.10, 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, S.107, K.140, P.163, T.164, L.166 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:P.163, B:L.166, B:L.166 Hydrogen bonds: B:M.14, B:V.15, B:N.40, B:L.41, B:L.42, B:A.64, B:L.166, B:L.166 Water bridges: B:G.10, B:G.13, B:G.16, B:R.36, B:R.36, B:R.36, B:R.36, B:A.63, B:L.105, B:S.107, B:E.136, B:K.140, B:H.170 Salt bridges: B:R.36

2 x UVW: ACETYLPHOSPHATE(Non-covalent)

UVW.2: 8 residues within 4Å: Chain A: G.67, G.68, I.69, V.70, A.71, S.176, N.177, S.178 6 PLIP interactions: 6 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 UVW.8: 8 residues within 4Å: Chain B: G.67, G.68, I.69, V.70, A.71, S.176, N.177, S.178 6 PLIP interactions: 6 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

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

TRS.3: 9 residues within 4Å: Chain A: A.77, D.78, Y.81, Q.82 Chain B: H.92, H.95, Y.150, Q.153, Y.154 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.92, B:Y.150, A:Q.82 Water bridges: B:Q.96, B:Q.96, B:Y.154, B:Y.154 TRS.6: 5 residues within 4Å: Chain A: S.17, R.21, P.169, H.170, W.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.21 TRS.9: 9 residues within 4Å: Chain A: H.92, H.95, Y.150, Q.153, Y.154 Chain B: A.77, D.78, Y.81, Q.82 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.92, A:Q.153, A:Q.153, A:Y.154, B:D.78, B:Q.82 Water bridges: A:Q.96, A:Q.96 TRS.12: 5 residues within 4Å: Chain B: S.17, R.21, P.169, H.170, W.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.21

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

SO4.4: 4 residues within 4Å: Chain A: H.11, R.12, R.20, T.35 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.11, A:R.12, A:R.20 SO4.5: 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: H.11, R.12, R.20, T.35 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.11, B:R.12, B:R.20 SO4.11: 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

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