SMTL ID : 3a06.1

Crystal structure of DXR from Thermooga maritia, in complex with fosmidomycin and NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 22 residues within 4Å: Chain A: G.10, A.11, T.12, G.13, S.14, I.15, H.37, S.38, N.39, T.58, A.92, V.93, S.94, S.97, A.115, N.116, K.117, E.118, D.142, M.192, I.196, M.254 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.15, A:I.196 Hydrogen bonds: A:G.10, A:T.12, A:T.12, A:T.12, A:G.13, A:S.14, A:S.14, A:S.14, A:I.15, A:H.37, A:S.38, A:N.39, A:V.93, A:S.94, A:S.94, A:S.97, A:K.117, A:G.193 Water bridges: A:G.16, A:T.58 pi-Stacking: A:H.37 NDP.2: 5 residues within 4Å: Chain A: K.24, I.29, R.30, L.31, F.50 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.24, A:R.30, A:L.31, A:L.31 Salt bridges: A:K.24, A:R.30 pi-Cation interactions: A:R.30 NDP.5: 23 residues within 4Å: Chain B: G.10, A.11, T.12, G.13, S.14, I.15, F.36, H.37, S.38, N.39, T.58, A.92, V.93, S.94, S.97, A.115, N.116, K.117, E.118, D.142, M.192, I.196, M.254 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.15 Hydrogen bonds: B:G.10, B:T.12, B:T.12, B:T.12, B:G.13, B:S.14, B:I.15, B:H.37, B:H.37, B:S.38, B:N.39, B:S.94, B:S.97, B:N.116, B:K.117, B:E.118 Water bridges: B:G.16 pi-Stacking: B:H.37

2 x FOM: 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID(Non-covalent)

FOM.3: 7 residues within 4Å: Chain A: T.162, A.163, S.164, W.190, S.200, N.205, K.206 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.164, A:S.200, A:N.205, A:K.206, A:K.206 Water bridges: A:G.165 FOM.6: 10 residues within 4Å: Chain B: E.144, T.162, A.163, S.164, G.165, W.190, M.192, S.200, N.205, K.206 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.164, B:S.164, B:G.165, B:S.200, B:N.205, B:K.206

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.142, S.143, E.209 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.142, A:E.209, H2O.3, H2O.3, H2O.3 MG.7: 3 residues within 4Å: Chain B: D.142, E.144, E.209 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.142, B:E.144, B:E.209, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takenoya, M. et al., Crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase from the hyperthermophile Thermotoga maritima for insights into the coordination of conformational changes and an inhibitor binding. J.Struct.Biol. (2010)

Release Date

2010-03-16

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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