SMTL ID : 1t2d.1

Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and oxalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 11 residues within 4Å: Chain A: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235, P.239 Ligands: NAD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.127 Water bridges: A:A.225 Salt bridges: A:R.95, A:R.95, A:R.158, A:H.182, A:H.182 OXL.4: 11 residues within 4Å: Chain B: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235, P.239 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.127 Water bridges: B:A.225 Salt bridges: B:R.95, B:R.95, B:R.158, B:H.182, B:H.182 OXL.7: 11 residues within 4Å: Chain C: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235, P.239 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.127 Water bridges: C:A.225 Salt bridges: C:R.95, C:R.95, C:R.158, C:H.182, C:H.182 OXL.10: 11 residues within 4Å: Chain D: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235, P.239 Ligands: NAD.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.127 Water bridges: D:A.225 Salt bridges: D:R.95, D:R.95, D:R.158, D:H.182, D:H.182

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

NAD.2: 29 residues within 4Å: Chain A: V.10, G.11, G.13, M.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, F.82, T.83, L.98, N.102, I.105, V.125, T.126, N.127, V.129, L.150, L.154, H.182, P.235, P.239 Ligands: OXL.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.15, A:V.125, A:L.150, A:L.154, A:P.239 Hydrogen bonds: A:G.13, A:M.14, A:I.15, A:I.36, A:Y.67, A:Y.67, A:G.81, A:F.82, A:N.102, A:N.127, A:N.127, A:L.150 Water bridges: A:G.16, A:T.83 NAD.5: 29 residues within 4Å: Chain B: V.10, G.11, G.13, M.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, F.82, T.83, L.98, N.102, I.105, V.125, T.126, N.127, V.129, L.150, L.154, H.182, P.235, P.239 Ligands: OXL.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.15, B:V.125, B:L.150, B:L.154, B:P.239 Hydrogen bonds: B:G.13, B:M.14, B:I.15, B:I.36, B:Y.67, B:Y.67, B:G.81, B:F.82, B:N.102, B:N.127, B:N.127, B:L.150 Water bridges: B:G.16, B:T.83 NAD.8: 29 residues within 4Å: Chain C: V.10, G.11, G.13, M.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, F.82, T.83, L.98, N.102, I.105, V.125, T.126, N.127, V.129, L.150, L.154, H.182, P.235, P.239 Ligands: OXL.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.15, C:V.125, C:L.150, C:L.154, C:P.239 Hydrogen bonds: C:G.13, C:M.14, C:I.15, C:I.36, C:Y.67, C:G.81, C:F.82, C:N.102, C:N.127, C:N.127, C:L.150 Water bridges: C:G.16 NAD.11: 29 residues within 4Å: Chain D: V.10, G.11, G.13, M.14, I.15, F.34, D.35, I.36, V.37, M.40, Y.67, T.79, A.80, G.81, F.82, T.83, L.98, N.102, I.105, V.125, T.126, N.127, V.129, L.150, L.154, H.182, P.235, P.239 Ligands: OXL.10 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.15, D:V.125, D:L.150, D:L.154, D:P.239 Hydrogen bonds: D:G.13, D:M.14, D:I.15, D:I.36, D:Y.67, D:G.81, D:F.82, D:N.102, D:N.127, D:N.127, D:L.150 Water bridges: D:G.16

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.156, K.160, N.175, A.176, H.177, V.257, I.259 Chain D: G.196 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.160, A:N.175, A:A.176, D:G.196 Water bridges: A:K.160, A:K.160, A:N.175, A:V.257, A:V.257 GOL.6: 8 residues within 4Å: Chain B: T.156, K.160, N.175, A.176, H.177, V.257, I.259 Chain C: G.196 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.160, B:N.175, B:A.176, C:G.196 Water bridges: B:K.160, B:K.160, B:N.175, B:V.257, B:V.257 GOL.9: 8 residues within 4Å: Chain B: G.196 Chain C: T.156, K.160, N.175, A.176, H.177, V.257, I.259 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.156, C:K.160, C:N.175, C:A.176, B:G.196 Water bridges: C:K.160, C:K.160, C:N.175, C:V.257, C:V.257 GOL.12: 8 residues within 4Å: Chain A: G.196 Chain D: T.156, K.160, N.175, A.176, H.177, V.257, I.259 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.156, D:K.160, D:N.175, D:A.176, A:G.196 Water bridges: D:K.160, D:K.160, D:N.175, D:V.257, D:V.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cameron, A. et al., Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity. J.Biol.Chem. (2004)

Release Date

2004-05-11

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-lactate dehydrogenase

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