SMTL ID : 3czm.1

T. Gondii bradyzoite-specific LDH (LDH2) in complex with NAD and OXQ

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: 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: OXQ.2 19 PLIP interactions: 19 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 NAD.3: 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: OXQ.4 18 PLIP interactions: 18 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, B:S.240 NAD.5: 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: OXQ.6 18 PLIP interactions: 18 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:E.112, C:S.240 NAD.7: 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: OXQ.8 19 PLIP interactions: 19 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, D:S.240

4 x OXQ: 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID(Non-covalent)

OXQ.2: 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.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.99, A:N.131, A:S.240, A:A.241 Salt bridges: A:R.99, A:R.162, A:H.186 pi-Stacking: A:W.97 OXQ.4: 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.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.99, B:N.131, B:S.240, B:A.241 Salt bridges: B:R.99, B:R.162, B:H.186 pi-Stacking: B:W.97 OXQ.6: 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.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.99, C:N.131, C:S.240, C:A.241 Salt bridges: C:R.99, C:R.162, C:H.186 pi-Stacking: C:W.97 OXQ.8: 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.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.99, D:N.131, D:S.240, D:A.241 Salt bridges: D:R.99, D:R.162, D:H.186 pi-Stacking: D:W.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilson, D.K. et al., T. Gondii bradyzoite-specific LDH (LDH2) in complex with NAD and OXQ. To be Published

Release Date

2009-06-02

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lactate dehydrogenase