SMTL ID : 4ooe.2 (1 other biounit)

M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase W203Y mutant bound to fosmidomycin and NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

FOM.1: 14 residues within 4Å: Chain A: D.166, S.167, E.168, A.191, S.192, H.215, Y.218, S.228, N.233, K.234, E.237, M.282 Ligands: MN.2, NDP.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:S.192, A:S.192, A:N.233, A:K.234, A:K.234 Water bridges: A:G.193, A:G.193 FOM.4: 16 residues within 4Å: Chain B: K.143, D.166, S.167, E.168, A.191, S.192, H.215, Y.218, M.220, S.228, N.233, K.234, E.237, M.282 Ligands: MN.5, NDP.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.143, B:S.167, B:S.192, B:S.228, B:N.233, B:K.234, B:K.234 Water bridges: B:G.193, B:G.193

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: K.143, D.166, E.168, E.237 Ligands: FOM.1, NDP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.166, A:E.168, A:E.168, A:E.237 MN.5: 7 residues within 4Å: Chain B: K.143, D.166, S.167, E.168, E.237 Ligands: FOM.4, NDP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.166, B:E.168, B:E.168, B:E.237

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

NDP.3: 28 residues within 4Å: Chain A: G.34, S.35, T.36, G.37, S.38, I.39, A.61, G.62, G.63, A.64, H.65, A.84, A.118, L.119, V.120, L.123, A.141, N.142, K.143, E.144, D.166, M.220, G.221, P.222, N.224, M.282 Ligands: FOM.1, MN.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.39 Hydrogen bonds: A:G.34, A:T.36, A:T.36, A:G.37, A:S.38, A:S.38, A:S.38, A:I.39, A:G.62, A:G.63, A:A.64, A:H.65, A:L.119, A:V.120, A:N.142, A:K.143, A:G.221 Water bridges: A:G.40, A:Q.42, A:Q.42, A:E.144, A:E.144, A:M.223, A:N.224, A:N.233 Salt bridges: A:H.65 NDP.6: 28 residues within 4Å: Chain B: G.34, S.35, T.36, G.37, S.38, I.39, A.61, G.62, G.63, A.64, H.65, A.84, A.118, L.119, V.120, L.123, A.141, N.142, K.143, E.144, D.166, M.220, G.221, P.222, N.224, M.282 Ligands: FOM.4, MN.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.39 Hydrogen bonds: B:G.34, B:T.36, B:T.36, B:T.36, B:G.37, B:S.38, B:S.38, B:S.38, B:I.39, B:G.62, B:G.63, B:A.64, B:H.65, B:L.119, B:N.142, B:K.143, B:G.221 Water bridges: B:G.40, B:Q.42, B:Q.42, B:A.61, B:E.144, B:E.144, B:M.223, B:N.224, B:N.233 Salt bridges: B:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kholodar, S.A. et al., Alteration of the Flexible Loop in 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase Boosts Enthalpy-Driven Inhibition by Fosmidomycin. Biochemistry (2014)

Release Date

2014-06-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

1-deoxy-D-xylulose 5-phosphate reductoisomerase

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