SMTL ID : 4okn.1 (1 other biounit)

Crystal structure of human muscle L-lactate dehydrogenase, ternary complex with NADH and oxalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 27 residues within 4Å: Chain A: V.25, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, A.97, R.98, Q.99, L.108, N.112, I.115, F.118, I.119, V.135, S.136, N.137, S.160, L.164, H.192, T.247, I.251 Ligands: OXL.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.30, A:I.251, A:I.251 Hydrogen bonds: A:V.27, A:A.29, A:V.30, A:V.52, A:G.96, A:G.96, A:A.97, A:V.135, A:N.137, A:N.137, A:S.160 Water bridges: A:G.28, A:G.31, A:Q.99 Salt bridges: A:R.98, A:R.98 NAI.7: 30 residues within 4Å: Chain C: V.25, G.26, G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, A.97, R.98, Q.99, L.108, N.112, I.115, F.118, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: OXL.8 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:V.30, C:I.251, C:I.251, C:I.251 Hydrogen bonds: C:A.29, C:V.30, C:V.52, C:K.56, C:K.56, C:G.96, C:G.96, C:A.97, C:Q.99, C:V.135, C:N.137, C:N.137, C:S.160 Water bridges: C:G.28, C:G.31 Salt bridges: C:K.56, C:R.98, C:R.98 NAI.10: 26 residues within 4Å: Chain D: G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, A.97, R.98, Q.99, N.112, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: OXL.11 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:V.30, D:I.251, D:I.251 Hydrogen bonds: D:A.29, D:V.30, D:V.52, D:K.56, D:K.56, D:G.96, D:G.96, D:A.97, D:Q.99, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31, D:Q.99 Salt bridges: D:K.56, D:R.98, D:R.98

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: NAI.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.99, A:N.137, A:T.247, A:T.247 Water bridges: A:A.237 Salt bridges: A:R.105, A:R.105, A:R.168, A:H.192, A:H.192 OXL.4: 6 residues within 4Å: Chain B: N.137, L.164, R.168, H.192, A.237, T.247 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.137 Water bridges: B:R.168, B:H.192 Salt bridges: B:R.168, B:H.192, B:H.192 OXL.8: 9 residues within 4Å: Chain C: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: NAI.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.137, C:T.247, C:T.247, C:T.247 Water bridges: C:R.168, C:A.237 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192 OXL.11: 9 residues within 4Å: Chain D: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: NAI.10 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.99, D:N.137, D:T.247 Water bridges: D:A.237 Salt bridges: D:R.105, D:R.105, D:R.168, D:H.192, D:H.192

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: N.163, S.166, R.170, P.271 Chain B: L.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.163, A:S.166 Salt bridges: A:R.170 SO4.5: 5 residues within 4Å: Chain B: R.170, H.185 Chain D: L.182, S.183, H.185 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Water bridges: B:R.170, B:R.170, B:H.185, D:H.185, D:A.206 Salt bridges: B:R.170, B:H.185, D:H.185 SO4.9: 6 residues within 4Å: Chain C: N.163, S.166, R.170, W.187, P.271 Chain D: L.69 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.166 Water bridges: C:D.257, C:H.270 Salt bridges: C:R.170 SO4.12: 6 residues within 4Å: Chain C: L.69 Chain D: N.163, S.166, R.170, W.187, P.271 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.163, D:S.166 Water bridges: D:H.270, D:H.270 Salt bridges: D:R.170

1 x KAN: KANAMYCIN A(Non-covalent)

KAN.6: 11 residues within 4Å: Chain B: D.51, V.52, Y.82, A.95, G.96, R.98, R.111, N.114, I.115, F.118, I.119 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.95 Hydrogen bonds: B:D.51, B:Y.82, B:Y.82, B:R.98, B:R.111, B:N.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolappan, S. et al., Structures of lactate dehydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms. Acta Crystallogr.,Sect.D (2015)

Release Date

2014-12-03

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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