SMTL ID : 4plv.1

Crystal structure of ancestral apicomplexan malate dehydrogenase with lactate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 23 residues within 4Å: Chain A: 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, A.237, P.241 Ligands: 2OP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.154, A:P.241 Hydrogen bonds: A:G.13, A:N.14, A:I.15, A:I.36, A:Y.67, A:G.81, A:N.127, A:N.127, A:M.150 Water bridges: A:G.16 NAI.3: 28 residues within 4Å: Chain B: 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: 2OP.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.15, B:V.125, B:P.241 Hydrogen bonds: B:N.14, B:N.14, B:I.15, B:I.36, B:Y.67, B:G.81, B:P.83, B:N.102, B:V.125, B:N.127, B:N.127 Water bridges: B:G.13, B:G.16, B:S.236 NAI.5: 26 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.82, P.83, L.98, N.102, I.105, V.125, T.126, N.127, M.150, L.154, H.182, A.237, P.241 Ligands: 2OP.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.15, C:L.154, C:P.241 Hydrogen bonds: C:G.13, C:N.14, C:N.14, C:I.15, C:I.36, C:G.81, C:I.82, C:N.102, C:V.125, C:N.127, C:N.127 Water bridges: C:N.14, C:G.16 NAI.7: 23 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, A.237, P.241 Ligands: 2OP.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.15, D:L.154, D:P.241 Hydrogen bonds: D:G.13, 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.16

4 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.2: 6 residues within 4Å: Chain A: N.127, L.154, R.158, H.182, G.225 Ligands: NAI.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.127, A:H.182 Salt bridges: A:R.158, A:H.182 2OP.4: 9 residues within 4Å: Chain B: W.93, R.95, N.127, L.154, R.158, H.182, G.225, A.237 Ligands: NAI.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.93 Hydrogen bonds: B:R.95, B:N.127, B:H.182 Water bridges: B:R.158, B:A.237 Salt bridges: B:R.95, B:R.158, B:H.182 2OP.6: 10 residues within 4Å: Chain C: W.93, R.95, N.127, L.154, R.158, H.182, G.225, S.236, A.237 Ligands: NAI.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.93 Hydrogen bonds: C:R.95, C:N.127, C:H.182 Water bridges: C:A.237 Salt bridges: C:R.95, C:R.158, C:H.182 2OP.8: 6 residues within 4Å: Chain D: N.127, R.158, H.182, G.225, A.237 Ligands: NAI.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.127, D:H.182 Water bridges: D:R.158, D:G.225, 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
A

B
B

C
C

D
D

malate dehydrogenase

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