SMTL ID : 5kvv.1

Structure of Malate Dehydrogenase in complex with NADH from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 28 residues within 4Å: Chain A: T.17, G.18, A.20, G.21, Q.22, I.23, L.48, E.49, I.50, A.53, V.94, G.95, A.96, R.97, P.98, L.108, I.115, Q.119, T.136, G.137, N.138, A.140, L.162, L.165, H.194, S.244, A.249 Ligands: TRS.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.23, A:L.165, A:A.249 Hydrogen bonds: A:G.18, A:Q.22, A:I.23, A:I.50, A:A.96, A:A.96, A:R.97, A:Q.119, A:N.138, A:N.138, A:L.162, A:S.244 Water bridges: A:Q.22, A:R.99 NAI.4: 25 residues within 4Å: Chain B: G.18, A.20, G.21, Q.22, I.23, L.48, E.49, I.50, A.53, V.94, G.95, A.96, R.97, P.98, I.115, Q.119, T.136, G.137, N.138, L.162, L.165, H.194, S.245, A.249 Ligands: SO4.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.23, B:L.165, B:A.249 Hydrogen bonds: B:G.18, B:Q.22, B:I.23, B:I.50, B:A.96, B:A.96, B:R.97, B:R.99, B:Q.119, B:N.138, B:N.138, B:L.162 Water bridges: B:G.21, B:G.24

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.279, Y.280, S.303, G.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.280, A:S.303, A:G.304 GOL.5: 2 residues within 4Å: Chain B: A.320, A.323 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 6 residues within 4Å: Chain A: R.99, N.138, R.169, H.194, G.234 Ligands: NAI.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.99, A:R.99, A:N.138, A:N.138, A:R.169, A:G.234 Water bridges: A:R.169, A:Q.198

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 7 residues within 4Å: Chain B: N.138, L.165, R.169, H.194, G.234, S.245 Ligands: NAI.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.138 Water bridges: B:R.169, B:G.234, B:G.234, B:S.245 Salt bridges: B:R.169, B:H.194 SO4.7: 4 residues within 4Å: Chain B: R.99, R.105, S.195, A.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.196 Water bridges: B:T.197 Salt bridges: B:R.99, B:R.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, Y.S. et al., Structure of Malate Dehydrogenase in complex with NADH from Mycobacterium tuberculosis. To Be Published

Release Date

2016-09-14

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase