SMTL ID : 1oc4.1

Lactate dehydrogenase from Plasmodium berghei

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: V.10, G.11, G.13, M.14, I.15, F.34, D.35, I.36, V.37, Y.67, T.79, A.80, G.81, F.82, T.83, N.102, I.105, I.109, V.125, T.126, N.127, V.129, L.150, L.154, H.182, P.235 Ligands: OXM.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.125, A:L.150, A:L.154 Hydrogen bonds: A:G.13, A:M.14, A:I.15, A:I.36, A:Y.67, A:G.81, A:F.82, A:N.102, A:V.125, A:N.127 NAD.4: 24 residues within 4Å: Chain B: G.11, S.12, 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, I.105, V.125, N.127, L.150, L.154, H.182, P.235 Ligands: OXM.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.15, B:V.125, B:L.154 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.127, B:L.150 Water bridges: B:G.16 NAD.7: 27 residues within 4Å: Chain C: V.10, G.11, G.13, M.14, I.15, F.34, D.35, I.36, V.37, Y.67, T.79, A.80, G.81, F.82, T.83, N.102, I.105, I.109, V.125, T.126, N.127, V.129, L.150, L.154, H.182, P.235 Ligands: OXM.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.125, C:L.150, C:L.154 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:V.125, C:N.127 NAD.10: 24 residues within 4Å: Chain D: G.11, S.12, 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, I.105, V.125, N.127, L.150, L.154, H.182, P.235 Ligands: OXM.11 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.15, D:V.125, D:L.154 Hydrogen bonds: D:G.13, D:M.14, D:I.15, D:I.36, D:Y.67, D:Y.67, D:G.81, D:F.82, D:N.127, D:L.150 Water bridges: D:G.16

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 10 residues within 4Å: Chain A: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.95, A:N.127, A:S.234 Salt bridges: A:R.95, A:R.158, A:H.182 OXM.5: 10 residues within 4Å: Chain B: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.95, B:S.234 Salt bridges: B:R.95, B:R.158, B:H.182 OXM.8: 10 residues within 4Å: Chain C: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.95, C:N.127, C:S.234 Salt bridges: C:R.95, C:R.158, C:H.182 OXM.11: 10 residues within 4Å: Chain D: W.93, R.95, N.127, L.154, R.158, H.182, A.225, S.234, P.235 Ligands: NAD.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.95, D:S.234 Salt bridges: D:R.95, D:R.158, D:H.182

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: T.156, K.160, N.175, A.176, H.177, V.257, I.259 Chain B: D.173, G.196 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.173, A:K.160, A:N.175, A:A.176 Water bridges: A:N.175, A:V.257, A:V.257 GOL.6: 7 residues within 4Å: Chain A: G.196 Chain B: T.156, K.160, N.175, A.176, V.257, I.259 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.156, B:T.156, B:K.160, B:K.160, B:N.175 Water bridges: B:V.257 GOL.9: 9 residues within 4Å: Chain C: T.156, K.160, N.175, A.176, H.177, V.257, I.259 Chain D: D.173, G.196 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.160, C:N.175, C:A.176, D:D.173 Water bridges: C:N.175, C:V.257, C:V.257 GOL.12: 7 residues within 4Å: Chain C: G.196 Chain D: T.156, K.160, N.175, A.176, V.257, I.259 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.156, D:T.156, D:K.160, D:K.160, D:N.175 Water bridges: D:V.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Winter, V.J. et al., Crystal Structure of Plasmodium Berghei Lactate Dehydrogenase Indicates the Unique Structural Differences of These Enzymes are Shared Across the Plasmodium Genus. Mol.Biochem.Parasitol. (2003)

Release Date

2003-09-18

Peptides

L-LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-LACTATE DEHYDROGENASE