SMTL ID : 7dbk.2 (1 other biounit)

Crystal structure of human LDHB in complex with NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 22 residues within 4Å: Chain A: 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, I.120, V.136, S.137, N.138, V.140, L.165, H.193, T.248, I.252 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.31, A:I.252, A:I.252 Hydrogen bonds: A:Q.30, A:V.31, A:V.53, A:G.97, A:N.113, A:V.136, A:N.138, A:N.138 Water bridges: A:G.29, A:Q.30, A:G.32, A:Q.100, A:N.138 Salt bridges: A:R.99, A:R.99 NAI.6: 22 residues within 4Å: Chain B: G.29, Q.30, V.31, D.52, V.53, L.54, Y.83, T.95, A.96, G.97, R.99, V.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.31, B:I.252, B:I.252 Hydrogen bonds: B:G.29, B:Q.30, B:V.31, B:V.53, B:G.97, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:G.32 Salt bridges: B:R.99 NAI.8: 23 residues within 4Å: Chain C: G.27, G.29, Q.30, V.31, D.52, V.53, L.54, Y.83, T.95, A.96, G.97, R.99, V.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.31 Hydrogen bonds: C:V.28, C:Q.30, C:V.31, C:V.53, C:Y.83, C:G.97, C:R.99, C:V.136, C:N.138, C:N.138 Water bridges: C:G.29, C:Q.30, C:G.32 NAI.10: 25 residues within 4Å: Chain D: 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, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:V.31, D:I.252 Hydrogen bonds: D:V.28, D:Q.30, D:V.31, D:V.53, D:Y.83, D:G.97, D:V.98, D:N.113, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:G.29, D:Q.30, D:G.32, D:R.106 Salt bridges: D:R.99, D:R.99

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: G.103, E.104, S.105, N.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.105, A:N.108 GOL.3: 12 residues within 4Å: Chain A: S.202, G.203, V.204, N.205, G.208, S.210 Chain C: S.202, G.203, V.204, N.205, G.208, S.210 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.202, C:N.205, C:S.210, A:V.204 Water bridges: A:L.211 GOL.4: 6 residues within 4Å: Chain A: G.41 Chain B: S.38, G.41, K.42, L.254 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.42 GOL.5: 8 residues within 4Å: Chain A: I.37, S.38, G.41, K.42, L.254 Chain B: I.37, G.41 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.41 GOL.7: 12 residues within 4Å: Chain B: S.202, G.203, V.204, N.205, G.208, S.210 Chain D: S.202, G.203, V.204, N.205, G.208, S.210 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:G.203, B:N.205, D:V.204 Water bridges: B:L.211, D:S.210, D:L.211 GOL.9: 8 residues within 4Å: Chain C: S.38, G.41 Chain D: I.37, S.38, G.41, K.42, L.254 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.37 Water bridges: D:K.42, D:K.42 GOL.11: 8 residues within 4Å: Chain C: I.37, S.38, G.41, K.42, L.254 Chain D: I.37, G.41 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) GOL.12: 6 residues within 4Å: Chain B: S.183, S.184, H.186 Chain D: R.171, H.186, W.188 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:S.184, B:H.186, D:R.171, D:R.171 Water bridges: B:A.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, S. et al., Identification of the first highly selective inhibitor of human lactate dehydrogenase B. Sci Rep (2021)

Release Date

2021-10-20

Peptides

L-lactate dehydrogenase B chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

L-lactate dehydrogenase B chain

Related Entries With Identical Sequence