SMTL ID : 1pzh.1

T.gondii LDH1 ternary complex with NAD and oxalate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 10 residues within 4Å: Chain A: W.99, R.101, N.133, L.160, R.164, H.188, G.231, S.242, A.243 Ligands: NAD.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.133 Water bridges: A:S.242, A:A.243, A:A.243 Salt bridges: A:R.101, A:R.101, A:R.164, A:H.188, A:H.188 OXL.3: 10 residues within 4Å: Chain B: W.99, R.101, N.133, L.160, R.164, H.188, G.231, S.242, A.243 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.133, B:S.242, B:S.242 Water bridges: B:A.243, B:A.243 Salt bridges: B:R.101, B:R.101, B:R.164, B:H.188, B:H.188 OXL.5: 10 residues within 4Å: Chain C: W.99, R.101, N.133, L.160, R.164, H.188, G.231, S.242, A.243 Ligands: NAD.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.133, C:S.242, C:S.242 Water bridges: C:A.243, C:A.243 Salt bridges: C:R.101, C:R.101, C:R.164, C:H.188, C:H.188 OXL.7: 10 residues within 4Å: Chain D: W.99, R.101, N.133, L.160, R.164, H.188, G.231, S.242, A.243 Ligands: NAD.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.133, D:S.242 Water bridges: D:A.243, D:A.243 Salt bridges: D:R.101, D:R.101, D:R.164, D:H.188, D:H.188

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

NAD.2: 27 residues within 4Å: Chain A: G.18, M.19, I.20, Y.39, D.40, V.41, V.42, M.45, T.85, A.86, G.87, L.88, T.89, L.104, N.108, I.111, V.131, T.132, N.133, L.135, M.156, A.157, L.160, H.188, A.243, P.247 Ligands: OXL.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.20, A:V.131, A:L.160, A:P.247 Hydrogen bonds: A:M.19, A:I.20, A:V.41, A:G.87, A:L.88, A:N.108, A:V.131, A:N.133, A:N.133 Water bridges: A:G.18, A:G.21, A:T.89, A:S.242, A:S.242 NAD.4: 27 residues within 4Å: Chain B: G.18, M.19, I.20, Y.39, D.40, V.41, V.42, M.45, T.85, A.86, G.87, L.88, T.89, L.104, N.108, I.111, V.131, T.132, N.133, L.135, M.156, A.157, L.160, H.188, A.243, P.247 Ligands: OXL.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.20, B:V.131, B:L.160, B:P.247 Hydrogen bonds: B:M.19, B:I.20, B:V.41, B:G.87, B:L.88, B:N.108, B:V.131, B:N.133, B:N.133 Water bridges: B:G.18, B:G.21, B:S.242 NAD.6: 28 residues within 4Å: Chain C: G.16, G.18, M.19, I.20, Y.39, D.40, V.41, V.42, M.45, T.85, A.86, G.87, L.88, T.89, L.104, N.108, I.111, V.131, T.132, N.133, L.135, M.156, A.157, L.160, H.188, A.243, P.247 Ligands: OXL.5 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.20, C:V.131, C:L.160, C:P.247 Hydrogen bonds: C:M.19, C:I.20, C:V.41, C:G.87, C:L.88, C:N.108, C:V.131, C:N.133, C:N.133 Water bridges: C:G.18, C:G.21, C:T.89, C:E.114, C:S.242 NAD.8: 27 residues within 4Å: Chain D: G.18, M.19, I.20, Y.39, D.40, V.41, V.42, M.45, T.85, A.86, G.87, L.88, T.89, L.104, N.108, I.111, V.131, T.132, N.133, L.135, M.156, A.157, L.160, H.188, A.243, P.247 Ligands: OXL.7 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.20, D:V.131, D:L.160, D:P.247 Hydrogen bonds: D:G.18, D:M.19, D:I.20, D:V.41, D:G.87, D:L.88, D:N.108, D:V.131, D:N.133, D:N.133 Water bridges: D:G.21, D:Y.72, D:Y.72, D:S.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavanagh, K.L. et al., Structure of Toxoplasma gondii LDH1: Active-Site Differences from Human Lactate Dehydrogenases and the Structural Basis for Efficient APAD+ Use. Biochemistry (2004)

Release Date

2004-02-24

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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