SMTL ID : 4plc.1

Crystal structure of ancestral apicomplexan lactate dehydrogenase with malate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 10 residues within 4Å: Chain A: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAI.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.97 Hydrogen bonds: A:R.99, A:R.99, A:N.131, A:H.186 Water bridges: A:R.162, A:A.241 Salt bridges: A:R.99, A:R.162, A:H.186 PYR.3: 10 residues within 4Å: Chain B: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.97 Hydrogen bonds: B:R.99, B:R.99, B:N.131, B:H.186 Water bridges: B:G.229, B:A.241 Salt bridges: B:R.99, B:R.162, B:H.186 PYR.5: 10 residues within 4Å: Chain C: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAI.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.97 Hydrogen bonds: C:R.99, C:R.99, C:N.131, C:H.186 Water bridges: C:R.162 Salt bridges: C:R.99, C:R.162, C:H.186 PYR.7: 10 residues within 4Å: Chain D: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAD.8 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.97 Hydrogen bonds: D:R.99, D:R.99, D:N.131, D:H.186 Water bridges: D:R.162, D:A.241 Salt bridges: D:R.99, D:R.162, D:H.186

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

NAI.2: 36 residues within 4Å: Chain A: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, V.113, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: PYR.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.19, A:I.129, A:P.245 Hydrogen bonds: A:G.17, A:M.18, A:I.19, A:V.40, A:G.85, A:L.86, A:L.86, A:N.106, A:E.112, A:N.131, A:N.131, A:M.154, A:H.186 Water bridges: A:G.20, A:T.87, A:T.87, A:S.240, A:S.240 NAI.6: 35 residues within 4Å: Chain C: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, V.113, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: PYR.5 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.19, C:I.129, C:P.245 Hydrogen bonds: C:G.17, C:M.18, C:I.19, C:V.40, C:G.85, C:L.86, C:L.86, C:N.106, C:E.112, C:N.131, C:N.131, C:H.186 Water bridges: C:G.20, C:T.87, C:S.240, C:S.240

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

NAD.4: 35 residues within 4Å: Chain B: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: PYR.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.19, B:I.129, B:P.245 Hydrogen bonds: B:G.17, B:M.18, B:I.19, B:V.40, B:G.85, B:L.86, B:L.86, B:N.106, B:E.112, B:N.131, B:N.131, B:M.154 Water bridges: B:G.20, B:T.87, B:S.240, B:S.240 NAD.8: 35 residues within 4Å: Chain D: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: PYR.7 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.19, D:I.129, D:P.245 Hydrogen bonds: D:G.17, D:M.18, D:I.19, D:V.40, D:G.85, D:L.86, D:L.86, D:N.106, D:E.112, D:N.131, D:N.131, D:M.154, D:H.186 Water bridges: D:S.16, D:G.20, D:K.48, D:W.97

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

lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

lactate dehydrogenase

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