SMTL ID : 4rcv.1

M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase bound to 1-deoxy-L-erythrulose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: K.143, D.166, E.168, E.237 Ligands: DE2.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.166, A:E.168, A:E.237 MN.5: 3 residues within 4Å: Chain B: D.166, E.168, E.237 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.166, B:E.168, B:E.237

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

NDP.2: 25 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, P.222, N.224, M.282 Ligands: DE2.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.39 Hydrogen bonds: A:G.34, A:T.36, 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:N.224 Water bridges: A:A.61, A:S.100, A:E.144, A:E.144, A:N.233 Salt bridges: A:H.65 NDP.6: 14 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.118, L.119, V.120 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.34, B:T.36, B:T.36, B:T.36, B:S.38, B:I.39, B:G.62, B:G.63, B:A.64, B:H.65, B:V.120 Water bridges: B:G.37, B:G.37 Salt bridges: B:H.65

1 x DE2: 1-deoxy-L-erythrulose(Non-covalent)

DE2.3: 12 residues within 4Å: Chain A: K.143, D.166, S.167, E.168, N.224, S.228, N.233, K.234, E.237 Ligands: MN.1, NDP.2, PO3.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.143, A:S.167, A:N.224, A:N.233, A:K.234

2 x PO3: PHOSPHITE ION(Non-covalent)

PO3.4: 6 residues within 4Å: Chain A: A.191, S.192, S.228, N.233, K.234 Ligands: DE2.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.192, A:N.233 Water bridges: A:G.193, A:G.193, A:S.228 Salt bridges: A:K.234 PO3.7: 7 residues within 4Å: Chain B: E.168, T.190, A.191, S.192, S.228, N.233, K.234 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.190, B:S.192, B:N.233 Salt bridges: B:K.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kholodar, S.A. et al., The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces. J.Am.Chem.Soc. (2015)

Release Date

2015-03-18

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