SMTL ID : 4oof.1

M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase W203F mutant bound to fosmidomycin and NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 27 residues within 4Å: Chain A: G.33, S.34, T.35, G.36, S.37, I.38, A.60, G.61, G.62, A.63, H.64, A.83, A.117, L.118, V.119, L.122, A.140, N.141, K.142, E.143, D.165, M.219, G.220, P.221, N.223, M.281 Ligands: FOM.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.38 Hydrogen bonds: A:G.33, A:T.35, A:T.35, A:G.36, A:S.37, A:S.37, A:I.38, A:G.61, A:G.62, A:A.63, A:H.64, A:L.118, A:V.119, A:N.141, A:K.142, A:G.220 Water bridges: A:G.39, A:Q.41, A:Q.41, A:E.143, A:E.143, A:M.222, A:N.223, A:N.232 Salt bridges: A:H.64 NDP.4: 28 residues within 4Å: Chain B: G.33, S.34, T.35, G.36, S.37, I.38, A.60, G.61, G.62, A.63, H.64, A.83, A.117, L.118, V.119, L.122, A.140, N.141, K.142, E.143, D.165, M.219, G.220, P.221, N.223, M.281 Ligands: MN.5, FOM.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.38 Hydrogen bonds: B:G.33, B:T.35, B:T.35, B:T.35, B:G.36, B:S.37, B:S.37, B:I.38, B:G.61, B:G.62, B:A.63, B:H.64, B:L.118, B:V.119, B:N.141, B:K.142, B:G.220 Water bridges: B:G.39, B:Q.41, B:Q.41, B:E.143, B:E.143, B:M.222, B:N.223, B:N.232 Salt bridges: B:H.64

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

MN.2: 6 residues within 4Å: Chain A: K.142, D.165, S.166, E.167, E.236 Ligands: FOM.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:E.167, A:E.167, A:E.236 MN.5: 7 residues within 4Å: Chain B: K.142, D.165, S.166, E.167, E.236 Ligands: NDP.4, FOM.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.165, B:E.167, B:E.167, B:E.236

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

FOM.3: 17 residues within 4Å: Chain A: K.142, D.165, S.166, E.167, A.190, S.191, H.214, F.217, M.219, N.223, S.227, N.232, K.233, E.236, M.281 Ligands: NDP.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.142, A:S.166, A:S.191, A:S.191, A:S.227, A:N.232, A:K.233 Water bridges: A:G.192, A:G.192 FOM.6: 18 residues within 4Å: Chain B: K.142, D.165, S.166, E.167, T.189, A.190, S.191, H.214, F.217, M.219, N.223, S.227, N.232, K.233, E.236, M.281 Ligands: NDP.4, MN.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.142, B:S.166, B:S.191, B:S.191, B:N.223, B:S.227, B:N.232, B:K.233 Water bridges: B:G.192, B:G.192

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
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase