SMTL ID : 7nrz.1 (3 other biounits)

Crystal structure of malate dehydrogenase from Trypanosoma cruzi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

27 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: V.126, V.155, S.156, L.157, L.158, H.185, M.235 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: L.157, G.160, T.164, Y.178, V.179, Y.259 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: V.37, G.38, P.40, A.60 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: E.285, R.286, R.287 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: G.8, D.35, V.37 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Y.259, P.276, L.288, P.289, I.290 Ligands: PGE.18 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: T.55, V.56 Chain B: R.165, N.169 Ligands: PEG.6, EDO.24 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: S.116, P.119, V.146 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.165, N.169, R.213 Chain B: S.47 Ligands: EDO.20 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.24, M.244, H.245, K.248 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: M.1, V.2, N.3, G.78, D.80 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: K.57, H.58 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: Y.178, H.245, M.257 Ligands: PEG.19 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: P.65, V.66, P.67, I.106, D.109 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: P.198, G.199 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: R.165, N.169 Chain B: I.54, T.55, V.56 Ligands: EDO.11 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: V.155, S.156, L.157, L.158, H.185, M.235 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: R.165, N.168, N.169, H.172 Chain B: A.52, G.53, I.54 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: Y.259, P.276, L.288, P.289, I.290 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: S.47 Chain B: R.165, N.169, R.213 Ligands: EDO.9 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain B: P.119, N.120, A.121, F.123, L.141, V.146, Y.147, N.148, K.151 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: L.157, G.160, T.164, Y.178, V.179, V.181, Y.259 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Q.15 Chain B: K.225, R.228, S.230, T.232 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain B: I.13, V.85, A.86, G.87, V.88, V.126, T.127, N.128, M.235 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: R.241 Chain B: D.50, R.51 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: G.11, D.35, V.37 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: M.1, N.3, G.78, D.80 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 10 residues within 4Å: Chain A: A.52, G.53, I.54, T.55 Chain B: R.165, N.168, N.169, H.172, V.175 Ligands: EDO.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.53, A:I.54, B:R.165 PEG.19: 5 residues within 4Å: Chain A: Y.178, T.255, P.256, M.257 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.178, A:Y.178, A:T.255, A:M.257 PEG.25: 4 residues within 4Å: Chain B: N.150, E.285, R.286, R.287 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.149, B:K.149, B:N.150, B:D.265, B:R.287, B:R.287

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 7 residues within 4Å: Chain A: R.23, F.27, D.50, R.51, A.52 Chain B: E.237, R.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.23, A:R.51, A:A.52 PGE.18: 7 residues within 4Å: Chain A: Y.178, P.180, S.195, Q.196, Y.259, P.292 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.259, A:Y.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sonani, R.R. et al., Distinct sequence and structural feature of trypanosoma malate dehydrogenase. Biochem.Biophys.Res.Commun. (2021)

Release Date

2022-02-16

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase

Related Entries With Identical Sequence