SMTL ID : 2pk3.1

Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x A2R: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

A2R.1: 18 residues within 4Å: Chain A: G.22, F.23, V.24, R.44, L.58, D.59, I.60, M.61, L.81, A.82, A.83, S.85, T.100, I.124, Y.152, K.156, H.182 Ligands: GDD.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:F.23, A:V.24, A:D.59, A:I.60, A:L.81, A:A.83, A:S.85, A:Y.152, A:Y.152, A:K.156 Water bridges: A:G.19, A:A.21, A:G.25, A:R.44, A:R.44, A:R.44, A:R.44, A:R.44, A:K.84, A:S.85, A:S.85, A:H.182, A:S.188 Salt bridges: A:R.44, A:K.156, A:H.182, A:H.182 pi-Cation interactions: A:R.44 A2R.3: 18 residues within 4Å: Chain B: G.22, F.23, V.24, R.44, L.58, D.59, I.60, M.61, L.81, A.82, A.83, S.85, T.100, I.124, Y.152, K.156, H.182 Ligands: GDD.4 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:F.23, B:V.24, B:N.45, B:D.59, B:I.60, B:L.81, B:A.83, B:S.85, B:Y.152, B:Y.152, B:K.156 Water bridges: B:G.19, B:G.22, B:G.22, B:G.25, B:R.44, B:N.45, B:K.84, B:S.85, B:T.100, B:H.182, B:Q.187, B:S.188, B:S.188 Salt bridges: B:R.44, B:K.156, B:H.182, B:H.182 pi-Cation interactions: B:R.44

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

GDD.2: 23 residues within 4Å: Chain A: S.85, V.87, S.126, S.127, Y.152, T.179, F.180, N.181, H.182, G.190, F.191, V.192, D.195, F.196, G.215, N.216, A.219, R.221, I.256, Q.279, R.281, E.284 Ligands: A2R.1 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.85, A:S.127, A:S.127, A:N.181, A:G.190, A:V.192, A:G.215, A:R.221, A:R.281, A:E.284 Water bridges: A:V.87, A:G.125, A:E.128, A:E.128, A:Y.152, A:T.179, A:F.180, A:N.181, A:H.182, A:Q.187, A:Q.187, A:N.216, A:Q.279, A:R.281, A:R.281, A:R.281 Salt bridges: A:D.195, A:R.281, A:R.281 GDD.4: 23 residues within 4Å: Chain B: S.85, V.87, S.126, S.127, Y.152, T.179, F.180, N.181, H.182, G.190, F.191, V.192, D.195, F.196, G.215, N.216, A.219, R.221, I.256, Q.279, R.281, E.284 Ligands: A2R.3 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:S.85, B:S.126, B:S.127, B:S.127, B:N.181, B:G.190, B:G.190, B:V.192, B:G.215, B:R.221, B:R.281, B:E.284 Water bridges: B:V.87, B:S.127, B:H.182, B:H.182, B:Q.187, B:Q.187, B:N.216, B:Q.279, B:R.281, B:R.281, B:R.281, B:R.281 Salt bridges: B:D.195, B:R.281, B:R.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

King, J.D. et al., The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway. Febs J. (2009)

Release Date

2008-03-25

Peptides

GDP-6-deoxy-D-lyxo-4-hexulose reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP-6-deoxy-D-lyxo-4-hexulose reductase