SMTL ID : 4ply.1 (1 other biounit)

Crystal structure of ancestral apicomplexan malate dehydrogenase with malate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 30 residues within 4Å: Chain A: I.10, G.11, G.13, N.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, I.82, P.83, L.98, N.102, I.105, V.125, T.126, N.127, L.129, M.150, L.154, H.182, S.236, A.237, P.241 Ligands: PYR.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.15, A:V.125, A:P.241 Hydrogen bonds: A:N.14, A:N.14, A:I.15, A:I.36, A:G.81, A:G.81, A:I.82, A:N.102, A:V.125, A:N.127, A:N.127 Water bridges: A:G.13, A:G.16, A:S.236, A:S.236, A:S.236, A:S.236 NAI.3: 27 residues within 4Å: Chain B: G.11, G.13, N.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, I.82, P.83, L.98, I.105, V.125, T.126, N.127, M.150, L.154, H.182, S.236, A.237, P.241 Ligands: PYR.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.15, B:L.154, B:P.241 Hydrogen bonds: B:G.13, B:N.14, B:N.14, B:I.15, B:I.36, B:G.81, B:I.82, B:V.125, B:N.127, B:N.127 Water bridges: B:G.16, B:S.236, B:S.236, B:S.236 NAI.5: 21 residues within 4Å: Chain C: G.13, N.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, I.105, V.125, T.126, N.127, L.129, M.150, L.154, H.182, P.241 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.154, C:P.241 Hydrogen bonds: C:G.13, C:N.14, C:I.15, C:I.36, C:Y.67, C:G.81, C:V.125, C:N.127 Water bridges: C:G.16 NAI.6: 24 residues within 4Å: Chain D: G.13, N.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, I.105, V.125, T.126, N.127, L.129, M.150, L.154, H.182, S.236, A.237, P.241 Ligands: PYR.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.15, D:V.125, D:L.154, D:P.241 Hydrogen bonds: D:N.14, D:N.14, D:I.15, D:I.36, D:G.81, D:V.125, D:N.127, D:N.127 Water bridges: D:G.13, D:G.16

3 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: W.93, R.95, N.127, R.158, H.182, G.225, S.236, A.237 Ligands: NAI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.93 Hydrogen bonds: A:R.95, A:N.127 Water bridges: A:R.158, A:R.158, A:A.237 Salt bridges: A:R.95, A:R.158, A:H.182 PYR.4: 9 residues within 4Å: Chain B: W.93, R.95, N.127, L.154, R.158, H.182, G.225, S.236 Ligands: NAI.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.93 Hydrogen bonds: B:R.95, B:N.127 Water bridges: B:D.155, B:G.225, B:A.237 Salt bridges: B:R.95, B:R.158, B:H.182 PYR.7: 5 residues within 4Å: Chain D: N.127, R.158, H.182, G.225 Ligands: NAI.6 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.127 Water bridges: D:A.237 Salt bridges: D:R.158, D:H.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boucher, J.I. et al., An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. Elife (2014)

Release Date

2014-07-02

Peptides

malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

malate dehydrogenase

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