SMTL ID : 1t2f.1

Human B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: G.29, Q.30, V.31, D.52, V.53, L.54, Y.83, T.95, G.97, V.98, R.99, N.113, V.116, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: OXQ.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.31, A:V.136, A:I.252, A:I.252 Hydrogen bonds: A:Q.30, A:V.31, A:V.53, A:L.54, A:Y.83, A:G.97, A:V.98, A:N.113, A:V.136, A:N.138, A:N.138, A:S.161 Salt bridges: A:R.99, A:R.99 NAD.3: 25 residues within 4Å: Chain B: V.28, G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, Q.100, V.116, I.120, V.136, S.137, N.138, S.161, L.165, H.193, Y.247, T.248, I.252 Ligands: OXQ.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.31, B:V.136, B:I.252, B:I.252 Hydrogen bonds: B:V.28, B:Q.30, B:V.31, B:G.97, B:V.98, B:Q.100, B:V.136, B:N.138, B:S.161 Water bridges: B:R.99, B:R.99, B:T.248 Salt bridges: B:R.99, B:R.99 NAD.5: 25 residues within 4Å: Chain C: G.27, V.28, G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, N.113, V.116, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: OXQ.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.31, C:I.252, C:I.252 Hydrogen bonds: C:V.28, C:G.29, C:Q.30, C:V.31, C:G.97, C:V.98, C:N.113, C:V.136, C:N.138, C:N.138, C:S.161 Salt bridges: C:R.99, C:R.99 NAD.7: 23 residues within 4Å: Chain D: V.28, G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, Q.100, V.136, S.137, N.138, S.161, L.165, H.193, Y.247, T.248, I.252 Ligands: OXQ.8 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.31, D:V.136, D:I.252 Hydrogen bonds: D:Q.30, D:V.31, D:V.53, D:G.97, D:G.97, D:V.98, D:Q.100, D:V.136, D:N.138, D:S.161 Water bridges: D:G.29, D:T.95 Salt bridges: D:R.99, D:R.99

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

OXQ.2: 9 residues within 4Å: Chain A: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.100, A:N.138, A:T.248 Water bridges: A:R.169 Salt bridges: A:R.106, A:R.169, A:H.193 OXQ.4: 9 residues within 4Å: Chain B: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.100, B:N.138, B:N.138, B:T.248, B:T.248 Salt bridges: B:R.106, B:R.169, B:H.193 OXQ.6: 9 residues within 4Å: Chain C: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAD.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.100, C:R.106, C:N.138 Salt bridges: C:R.106, C:R.169, C:H.193 OXQ.8: 9 residues within 4Å: Chain D: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAD.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.100, D:R.106, D:N.138, D:T.248, D:T.248 Salt bridges: D:R.106, D:R.169, D:H.193

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 B chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase B chain