SMTL ID : 1kc1.1

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.190 Chain B: E.15, E.190 Ligands: MG.4 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: E.15, E.190 Chain B: E.190 Ligands: MG.1 No protein-ligand interaction detected (PLIP)

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

SO4.2: 2 residues within 4Å: Chain A: K.158 Chain B: T.295 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.158 SO4.5: 2 residues within 4Å: Chain A: T.295 Chain B: K.158 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.158

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.3: 20 residues within 4Å: Chain A: T.9, G.10, Q.11, V.12, V.31, G.38, D.39, F.40, A.61, A.62, A.63, T.65, L.80, Y.102, S.103, T.104, Y.128, K.132, T.151, V.154 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.154 Hydrogen bonds: A:Q.11, A:Q.11, A:V.12, A:D.39, A:D.39, A:F.40, A:A.63, A:Y.128, A:K.132, A:V.154 Water bridges: A:G.7, A:G.10, A:G.13, A:V.31, A:H.101, A:Y.102, A:W.153 NDP.6: 20 residues within 4Å: Chain B: T.9, G.10, Q.11, V.12, V.31, G.38, D.39, F.40, A.61, A.62, A.63, T.65, L.80, Y.102, S.103, T.104, Y.128, K.132, T.151, V.154 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.154 Hydrogen bonds: B:Q.11, B:Q.11, B:V.12, B:D.39, B:D.39, B:F.40, B:A.63, B:Y.128, B:K.132, B:V.154 Water bridges: B:G.7, B:G.10, B:G.13, B:V.31, B:H.101, B:Y.102, B:W.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blankenfeldt, W. et al., Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode. Structure (2002)

Release Date

2002-06-28

Peptides

dTDP-glucose oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

dTDP-glucose oxidoreductase

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