SMTL ID : 5zjd.1 (1 other biounit)

Lactate dehydrogenase with NADH and MLA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 26 residues within 4Å: Chain A: V.33, G.34, A.35, V.36, D.57, V.58, I.59, K.62, T.100, A.101, G.102, A.103, R.104, N.118, I.121, I.125, V.141, S.142, N.143, V.145, S.166, L.170, H.198, T.253, I.257 Ligands: MLI.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.36, A:I.257, A:I.257 Hydrogen bonds: A:V.33, A:A.35, A:V.36, A:V.58, A:K.62, A:K.62, A:G.102, A:G.102, A:A.103, A:N.118, A:V.141, A:N.143, A:N.143, A:S.166 Water bridges: A:G.37, A:R.104 Salt bridges: A:K.62, A:R.104, A:R.104 NAI.3: 26 residues within 4Å: Chain B: G.32, G.34, A.35, V.36, D.57, V.58, I.59, K.62, K.86, T.100, A.101, G.102, A.103, R.104, N.118, I.121, I.125, V.141, S.142, N.143, S.166, L.170, H.198, T.253, I.257 Ligands: MLI.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.36, B:I.257, B:I.257 Hydrogen bonds: B:A.35, B:V.36, B:V.58, B:K.62, B:K.62, B:K.86, B:G.102, B:A.103, B:N.118, B:V.141, B:N.143, B:N.143 Water bridges: B:G.34, B:G.37, B:R.104 Salt bridges: B:K.62, B:R.104, B:R.104 NAI.5: 25 residues within 4Å: Chain C: G.32, V.33, G.34, A.35, V.36, D.57, V.58, I.59, T.100, A.101, G.102, R.104, Q.105, I.121, F.124, I.125, V.141, S.142, N.143, S.166, L.170, H.198, T.253, I.257 Ligands: MLI.6 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:V.36 Hydrogen bonds: C:V.33, C:G.34, C:A.35, C:V.36, C:V.58, C:G.102, C:R.104, C:Q.105, C:V.141, C:N.143, C:N.143, C:S.166 Water bridges: C:G.37, C:Y.88, C:Y.88 Salt bridges: C:R.104, C:R.104 NAI.7: 27 residues within 4Å: Chain D: V.31, G.34, A.35, V.36, D.57, V.58, I.59, K.62, T.100, A.101, G.102, A.103, R.104, N.118, I.121, F.124, I.125, V.141, S.142, N.143, V.145, S.166, L.170, H.198, T.253, I.257 Ligands: MLI.8 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:V.36, D:V.141, D:I.257, D:I.257 Hydrogen bonds: D:V.33, D:A.35, D:V.36, D:V.58, D:G.102, D:A.103, D:N.118, D:V.141, D:N.143, D:N.143, D:S.166 Water bridges: D:G.34, D:G.37, D:K.62, D:K.62, D:R.104, D:R.104, D:Q.105 Salt bridges: D:K.62, D:R.104, D:R.104

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 9 residues within 4Å: Chain A: Q.105, R.111, N.143, L.170, R.174, H.198, A.243, T.253 Ligands: NAI.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.243 Hydrogen bonds: A:N.143 Water bridges: A:T.253 Salt bridges: A:R.111, A:R.111, A:R.174, A:H.198, A:H.198 MLI.4: 9 residues within 4Å: Chain B: Q.105, R.111, N.143, L.170, R.174, H.198, A.243, T.253 Ligands: NAI.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.143, B:T.253, B:T.253 Salt bridges: B:R.111, B:R.111, B:R.174, B:H.198, B:H.198 MLI.6: 9 residues within 4Å: Chain C: R.111, N.143, L.170, R.174, H.198, A.243, I.247, T.253 Ligands: NAI.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.247 Hydrogen bonds: C:N.143 Salt bridges: C:R.111, C:R.174, C:H.198, C:H.198 MLI.8: 9 residues within 4Å: Chain D: Q.105, R.111, N.143, L.170, R.174, H.198, A.243, T.253 Ligands: NAI.7 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.170 Hydrogen bonds: D:N.143, D:T.253, D:T.253 Salt bridges: D:R.111, D:R.111, D:R.174, D:H.198, D:H.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, T.-W. et al., Machilin A Inhibits Tumor Growth and Macrophage M2 Polarization Through the Reduction of Lactic Acid. Cancers (Basel) (2019)

Release Date

2019-07-24

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase A chain

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