SMTL ID : 4hcx.1

Structure of ICDH-1 from M.tuberculosis complexed with NADPH & Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.278, D.282 Chain B: D.255 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.278, A:D.278, A:D.282, B:D.255, H2O.5, H2O.7 MN.4: 3 residues within 4Å: Chain A: D.255 Chain B: D.278, D.282 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.255, B:D.278, B:D.278, H2O.1, H2O.12

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

NDP.2: 20 residues within 4Å: Chain A: K.75, A.77, T.78, I.79, T.80, R.85, N.99, E.309, A.310, H.312, G.313, T.314, V.315, T.316, R.317, H.318, S.329, T.330, N.331, D.378 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.75, A:T.78, A:T.78, A:T.80, A:T.80, A:T.80, A:R.85, A:R.85, A:N.99, A:G.313, A:G.313, A:T.314, A:V.315, A:R.317, A:N.331, A:N.331 Water bridges: A:R.317, A:R.317, A:R.317, A:H.318 Salt bridges: A:R.317, A:H.318 NDP.5: 19 residues within 4Å: Chain B: K.75, A.77, T.78, I.79, T.80, R.85, N.99, E.309, A.310, H.312, G.313, T.314, V.315, T.316, H.318, S.329, T.330, N.331, D.378 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.75, B:T.78, B:T.78, B:T.80, B:T.80, B:R.85, B:R.85, B:N.99, B:G.313, B:G.313, B:T.314, B:V.315, B:N.331, B:N.331 Water bridges: B:T.78, B:H.318 Salt bridges: B:H.318

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: F.138, G.139, R.143 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: A.137, F.138, G.139, R.143 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quartararo, C.E. et al., Structural, Kinetic and Chemical Mechanism of Isocitrate Dehydrogenase-1 from Mycobacterium tuberculosis. Biochemistry (2013)

Release Date

2013-02-27

Peptides

Isocitrate dehydrogenase [NADP]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP]