SMTL ID : 7qoz.2 (1 other biounit)

Crystal structure of NAD-bound glycosomal malate dehydrogenase from Trypanosoma cruzi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 24 residues within 4Å: Chain A: A.18, G.19, G.20, I.21, Y.42, D.43, V.44, V.45, V.93, A.94, G.95, P.97, N.111, I.114, L.118, V.134, T.135, N.136, V.138, V.163, H.193, A.239, T.240, M.243 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.21, A:M.243 Hydrogen bonds: A:A.18, A:G.20, A:I.21, A:V.44, A:G.95, A:N.111, A:N.136, A:N.136, A:V.163 Water bridges: A:G.19, A:G.22, A:R.98, A:R.98 NAD.2: 23 residues within 4Å: Chain B: A.18, G.19, G.20, I.21, Y.42, D.43, V.44, V.45, V.93, A.94, G.95, P.97, I.114, L.118, V.134, T.135, N.136, V.138, V.163, H.193, A.239, T.240, M.243 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.21 Hydrogen bonds: B:A.18, B:G.20, B:I.21, B:V.44, B:G.95, B:N.136, B:N.136, B:V.163 Water bridges: B:G.22, B:V.96, B:R.98, B:R.98 NAD.3: 24 residues within 4Å: Chain C: G.16, A.18, G.19, G.20, I.21, Y.42, D.43, V.44, V.45, V.93, A.94, G.95, I.114, L.118, V.134, T.135, N.136, V.163, L.166, H.193, S.238, A.239, T.240, M.243 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.21 Hydrogen bonds: C:A.18, C:G.20, C:I.21, C:V.44, C:A.94, C:G.95, C:N.136, C:N.136, C:V.163 Water bridges: C:G.22 NAD.4: 23 residues within 4Å: Chain D: G.16, A.18, G.19, G.20, I.21, Y.42, D.43, V.44, V.45, V.93, A.94, G.95, I.114, L.118, V.134, T.135, N.136, V.138, V.163, H.193, A.239, T.240, M.243 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.21 Hydrogen bonds: D:A.18, D:G.20, D:I.21, D:V.44, D:A.94, D:G.95, D:V.134, D:N.136, D:N.136 Water bridges: D:G.19, D:G.22, D:D.117, D:D.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: Q.204, Y.267, P.284, L.296, P.297, I.298 Chain D: P.206, G.207, P.208 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:G.207, A:Q.204, A:P.297 Water bridges: A:Y.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sonani, R.R. et al., Crystal structure of NAD-bound glycosomal malate dehydrogenase from Trypanosoma cruzi. To Be Published

Release Date

2023-07-12

Peptides

Malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

C
H

D
F

Malate dehydrogenase

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