SMTL ID : 6cep.1

Sus scrofa heart L-lactate dehydrogenase ternary complex with NADH and oxamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: G.28, G.30, Q.31, V.32, D.53, V.54, L.55, T.96, A.97, G.98, V.99, R.100, N.114, V.117, I.121, V.137, S.138, N.139, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.32, A:I.253, A:I.253 Hydrogen bonds: A:Q.31, A:V.32, A:V.54, A:G.98, A:V.99, A:N.114, A:V.137, A:N.139, A:N.139, A:S.162 Water bridges: A:Q.31, A:G.33, A:R.100, A:Q.101 Salt bridges: A:R.100, A:R.100 NAD.3: 23 residues within 4Å: Chain B: V.29, G.30, Q.31, V.32, D.53, V.54, L.55, T.96, A.97, G.98, V.99, R.100, V.117, I.121, V.137, S.138, N.139, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.32, B:I.253 Hydrogen bonds: B:V.29, B:Q.31, B:V.32, B:V.54, B:G.98, B:V.99, B:V.137, B:N.139, B:S.162 Water bridges: B:G.30, B:G.33, B:R.100, B:N.139 Salt bridges: B:R.100, B:R.100 NAD.5: 23 residues within 4Å: Chain C: G.30, Q.31, V.32, D.53, V.54, L.55, T.96, A.97, G.98, V.99, R.100, N.114, V.117, I.121, V.137, S.138, N.139, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.6 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:V.32, C:I.253, C:I.253 Hydrogen bonds: C:Q.31, C:V.32, C:V.54, C:Y.84, C:G.98, C:V.99, C:N.114, C:V.137, C:N.139, C:N.139, C:S.162 Water bridges: C:G.30, C:G.33, C:R.100, C:Q.101 Salt bridges: C:R.100, C:R.100 NAD.7: 23 residues within 4Å: Chain D: V.29, G.30, Q.31, V.32, D.53, V.54, L.55, T.96, A.97, G.98, V.99, V.117, F.120, I.121, V.137, S.138, N.139, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.32 Hydrogen bonds: D:V.29, D:Q.31, D:V.32, D:V.54, D:G.98, D:V.137, D:N.139, D:N.139, D:S.162 Water bridges: D:G.30, D:Q.31, D:G.33

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 9 residues within 4Å: Chain A: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.107, A:N.139, A:T.249 Water bridges: A:T.249 Salt bridges: A:R.107, A:R.170, A:H.194 OXM.4: 7 residues within 4Å: Chain B: N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.249, B:T.249, B:T.249 Water bridges: B:T.249 Salt bridges: B:R.170, B:H.194 OXM.6: 9 residues within 4Å: Chain C: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.107, C:N.139, C:T.249 Water bridges: C:T.249 Salt bridges: C:R.107, C:R.170, C:H.194 OXM.8: 6 residues within 4Å: Chain D: N.139, R.170, H.194, A.239, T.249 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.139, D:T.249, D:T.249 Salt bridges: D:R.170, D:H.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, B.A. et al., Small molecule cores demonstrate non-competitive inhibition of lactate dehydrogenase. Medchemcomm (2018)

Release Date

2018-06-27

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