SMTL ID : 7qoz.1 (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: 26 residues within 4Å: Chain A: G.16, 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, L.166, H.193, A.239, T.240, M.243 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.21 Hydrogen bonds: A:A.18, A:G.20, A:I.21, A:V.44, A:G.95, A:N.111, A:N.136, A:H.193 Water bridges: A:G.19, A:G.22, A:R.98, A:R.98 NAD.4: 24 residues within 4Å: Chain B: 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 Ligands: GOL.5 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:A.94, B:G.95, B:V.134, B:N.136, B:N.136 Water bridges: B:G.19, B:G.22, B:S.238 NAD.6: 25 residues within 4Å: Chain C: G.16, A.18, G.19, G.20, I.21, Y.42, D.43, V.44, V.93, A.94, G.95, N.111, I.114, L.118, V.134, T.135, N.136, V.138, V.163, H.193, A.239, T.240, M.243 Ligands: GOL.7, GOL.8 13 PLIP interactions: 13 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.111, C:V.134, C:N.136, C:N.136 Water bridges: C:G.22, C:S.238 NAD.10: 23 residues within 4Å: Chain D: 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 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:G.95, D:N.111, D:N.136, D:N.136, D:H.193 Water bridges: D:G.19, D:G.22, D:R.98, D:R.98

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.206, G.207 Chain B: Q.204, L.296, P.297, I.298, G.299 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.207, B:Q.204 GOL.3: 7 residues within 4Å: Chain A: Q.204, L.296, P.297, I.298, G.299 Chain B: P.206, G.207 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.204, B:G.207 GOL.5: 6 residues within 4Å: Chain B: G.95, V.96, P.97, N.111, S.238 Ligands: NAD.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.111, B:S.238 Water bridges: B:G.95, B:S.238 GOL.7: 5 residues within 4Å: Chain C: R.170, G.226, S.238, A.239 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.170, C:A.239 Water bridges: C:N.136 GOL.8: 6 residues within 4Å: Chain C: G.95, V.96, P.97, N.111, S.238 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.96, C:N.111 Water bridges: C:S.238, C:S.238, C:S.238 GOL.9: 9 residues within 4Å: Chain C: P.206, G.207, P.208 Chain D: Q.204, P.284, L.296, P.297, I.298, G.299 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.204, D:P.297, C:G.207 Water bridges: D: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
A

B
B

C
C

D
D

Malate dehydrogenase

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