SMTL ID : 3a14.1

Crystal structure of DXR from Thermotoga maritima, in complex with 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: 6 residues within 4Å: Chain A: K.24, I.29, R.30, L.31, E.49, F.50 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.24, A:R.30, A:L.31, A:L.31 Salt bridges: A:R.30 pi-Cation interactions: A:R.30 NDP.2: 22 residues within 4Å: Chain A: 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, I.196, M.254 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.15 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:H.37, A:S.38, A:N.39, A:T.58, A:V.93, A:S.94, A:S.94, A:S.97, A:K.117 Water bridges: A:G.16, A:S.97 pi-Stacking: A:H.37 NDP.5: 21 residues within 4Å: Chain B: 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, M.254 22 PLIP interactions: 22 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:V.93, B:S.94, B:S.97, B:N.116, B:K.117, B:M.192 Water bridges: B:S.14, B:G.16 pi-Stacking: B:H.37, B:H.37

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.142, E.144, E.209 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.142, A:E.144, A:E.209, H2O.3, H2O.3 MG.6: 3 residues within 4Å: Chain B: D.142, E.144, E.209 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.142, B:E.209, H2O.7, H2O.7

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 8 residues within 4Å: Chain A: T.162, A.163, S.164, D.199, S.200, M.203, N.205, K.206 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.163, A:M.203, A:N.205, A:K.206 Hydrogen bonds: A:N.205, A:K.206 Water bridges: A:K.206 MPD.7: 8 residues within 4Å: Chain B: T.162, A.163, S.164, D.199, S.200, M.203, N.205, K.206 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.205, B:K.206, B:K.206 Hydrogen bonds: B:S.164, B:S.164, B:G.165 Water bridges: B:S.164

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

2010-04-07

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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