SMTL ID : 1sow.1

T. gondii bradyzoite-specific LDH (LDH2) in 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.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.131, A:S.240, A:S.240 Water bridges: A:R.99, A:A.241 Salt bridges: A:R.99, A:R.99, A:R.162, A:H.186, A:H.186 OXL.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 Hydrogen bonds: B:N.131, B:S.240, B:S.240 Water bridges: B:A.241, B:A.241 Salt bridges: B:R.99, B:R.99, B:R.162, B:H.186, B:H.186 OXL.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: NAD.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.131, C:S.240, C:S.240 Water bridges: C:R.99, C:A.241 Salt bridges: C:R.99, C:R.99, C:R.162, C:H.186, C:H.186 OXL.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 Hydrogen bonds: D:N.131, D:S.240, D:S.240 Water bridges: D:A.241, D:A.241 Salt bridges: D:R.99, D:R.99, D:R.162, D:H.186, D:H.186

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

NAD.2: 29 residues within 4Å: Chain A: G.15, G.17, M.18, I.19, 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.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, A.241, P.245 Ligands: OXL.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.19, A:V.129, A:L.158, A:P.245 Hydrogen bonds: A:M.18, A:I.19, A:V.40, A:G.85, A:L.86, A:N.106, A:E.112, A:V.129, A:N.131, A:N.131 Water bridges: A:G.17, A:G.20, A:T.87, A:T.87, A:S.240, A:S.240, A:S.240 NAD.4: 29 residues within 4Å: Chain B: G.15, G.17, M.18, I.19, 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.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, A.241, P.245 Ligands: OXL.3 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.19, B:V.129, B:L.158, B:P.245 Hydrogen bonds: B:M.18, B:I.19, B:V.40, B:G.85, B:L.86, B:N.106, B:E.112, B:V.129, B:N.131, B:N.131 Water bridges: B:G.17, B:G.20, B:S.240 NAD.6: 29 residues within 4Å: Chain C: G.15, G.17, M.18, I.19, 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.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, A.241, P.245 Ligands: OXL.5 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.19, C:V.129, C:L.158, C:P.245 Hydrogen bonds: C:M.18, C:I.19, C:V.40, C:G.85, C:L.86, C:N.106, C:E.112, C:V.129, C:N.131, C:N.131 Water bridges: C:G.17, C:G.20, C:T.87, C:S.240, C:S.240, C:S.240 NAD.8: 29 residues within 4Å: Chain D: G.15, G.17, M.18, I.19, 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.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, A.241, P.245 Ligands: OXL.7 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.19, D:V.129, D:L.158, D:P.245 Hydrogen bonds: D:M.18, D:I.19, D:V.40, D:G.85, D:L.86, D:N.106, D:E.112, D:V.129, D:N.131, D:N.131 Water bridges: D:G.17, D:G.20, D:T.87, D:S.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavanagh, K.L. et al., Structure of apo and ternary forms of Toxoplasma gondii LDH2. To be Published

Release Date

2005-03-15

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lactate dehydrogenase

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