SMTL ID : 3anm.1

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with 5-phenylpyridin-2-ylmethylphosphonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SYD: [(5-phenylpyridin-2-yl)methyl]phosphonic acid(Non-covalent)

SYD.1: 13 residues within 4Å: Chain A: E.162, G.195, S.196, H.219, N.221, W.222, S.232, N.237, K.238, P.262, Q.263, S.264, P.284 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.221, A:W.222, A:W.222, A:W.222, A:P.284 Hydrogen bonds: A:E.162, A:E.162, A:S.196, A:S.232, A:K.238 Water bridges: A:G.197 pi-Stacking: A:W.222 SYD.3: 13 residues within 4Å: Chain B: E.162, G.195, S.196, H.219, N.221, W.222, M.224, S.232, N.237, K.238, Q.263, S.264, P.284 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.221, B:W.222, B:W.222, B:P.284 Hydrogen bonds: B:E.162, B:S.196, B:S.232, B:N.237, B:K.238 Water bridges: B:G.197, B:K.238

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

NDP.2: 22 residues within 4Å: Chain A: G.18, S.19, T.20, G.21, S.22, I.23, V.44, A.45, G.46, K.47, N.48, D.67, A.110, I.111, V.112, A.115, A.133, N.134, K.135, E.136, D.160, M.286 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.23, A:D.160 Hydrogen bonds: A:G.18, A:T.20, A:T.20, A:T.20, A:G.21, A:S.22, A:I.23, A:G.46, A:K.47, A:N.48, A:D.67, A:I.111, A:V.112, A:N.134, A:K.135 Water bridges: A:G.24, A:D.67, A:D.67 NDP.4: 20 residues within 4Å: Chain B: G.18, S.19, T.20, G.21, S.22, I.23, A.45, G.46, K.47, N.48, D.67, A.110, I.111, V.112, A.115, A.133, N.134, K.135, D.160, M.286 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.23, B:D.160 Hydrogen bonds: B:G.18, B:T.20, B:T.20, B:T.20, B:G.21, B:S.22, B:I.23, B:G.46, B:K.47, B:N.48, B:D.67, B:I.111, B:V.112, B:K.135 Water bridges: B:S.22, B:S.22, B:G.24, B:G.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, L. et al., Structures of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase/Lipophilic Phosphonate Complexes. ACS Med Chem Lett (2011)

Release Date

2011-02-23

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase

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