SMTL ID : 3h3f.1 (1 other biounit)

Rabbit muscle L-lactate dehydrogenase in complex with NADH and oxamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 20 residues within 4Å: Chain A: G.26, G.28, A.29, V.30, D.51, V.52, M.53, T.94, A.95, G.96, I.115, I.119, V.135, S.136, N.137, S.160, H.192, T.247, I.251 Ligands: OXM.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.30, A:V.135, A:I.251 Hydrogen bonds: A:A.29, A:V.30, A:V.52, A:G.96, A:V.135, A:N.137, A:N.137, A:S.160 Water bridges: A:G.28, A:T.94, A:G.96 NAI.4: 24 residues within 4Å: Chain B: G.26, G.28, A.29, V.30, D.51, V.52, M.53, K.56, T.94, A.95, G.96, A.97, R.98, L.108, I.115, V.135, S.136, N.137, S.160, L.164, H.192, T.247, I.251 Ligands: OXM.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.30, B:I.251, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:K.56, B:K.56, B:G.96, B:V.135, B:N.137, B:N.137, B:S.160 Water bridges: B:G.28, B:G.31, B:R.98, B:Q.99 Salt bridges: B:K.56, B:R.98, B:R.98 NAI.7: 25 residues within 4Å: Chain C: G.26, G.28, A.29, V.30, D.51, V.52, M.53, K.56, T.94, A.95, G.96, A.97, R.98, I.115, F.118, I.119, V.135, S.136, N.137, S.160, L.164, H.192, T.247, I.251 Ligands: OXM.8 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:V.30, C:V.135, 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:A.97, C:Q.99, C:N.112, C:V.135, C:N.137, C:N.137, C:S.160 Water bridges: C:G.28, C:G.31, C:K.56, C:Y.82 Salt bridges: C:K.56, C:R.98, C:R.98 NAI.11: 24 residues within 4Å: Chain D: G.26, V.27, G.28, A.29, V.30, G.31, D.51, V.52, M.53, Y.82, T.94, A.95, G.96, I.115, F.118, I.119, V.135, S.136, N.137, V.139, S.160, H.192, I.251 Ligands: OXM.12 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.135, D:I.251 Hydrogen bonds: D:G.28, D:A.29, D:V.30, D:G.31, D:D.51, D:V.52, D:T.94, D:N.137, D:N.137, D:N.137, D:S.160

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 6 residues within 4Å: Chain A: N.137, R.168, H.192, A.237, T.247 Ligands: NAI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.137, A:H.192, A:T.247, A:T.247 Salt bridges: A:R.168 OXM.5: 8 residues within 4Å: Chain B: Q.99, R.105, N.137, R.168, H.192, A.237, T.247 Ligands: NAI.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.99, B:R.105, B:N.137, B:T.247 Water bridges: B:R.105, B:T.247 Salt bridges: B:R.105, B:R.168, B:H.192 OXM.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 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.99, C:R.105, C:N.137, C:T.247, C:T.247 Water bridges: C:T.247 Salt bridges: C:R.105, C:R.168, C:H.192 OXM.12: 6 residues within 4Å: Chain D: N.137, D.165, R.168, H.192, A.237 Ligands: NAI.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.137 Water bridges: D:R.168 Salt bridges: D:R.168, D:H.192

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: M.40, D.42, F.70, R.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.40 Water bridges: A:R.72 ACT.6: 3 residues within 4Å: Chain B: Y.280, K.304, V.305 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.280, B:K.304 Hydrogen bonds: B:V.305 ACT.9: 6 residues within 4Å: Chain C: N.87, S.88, S.127, P.128, H.129, C.130 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.129 Hydrogen bonds: C:N.87, C:H.129 Salt bridges: C:H.129 ACT.10: 3 residues within 4Å: Chain C: K.242, L.243 Chain D: D.55 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.55, D:D.55 ACT.13: 1 residues within 4Å: Chain D: K.316 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.316 ACT.14: 3 residues within 4Å: Chain D: G.281, E.312 Ligands: ACT.15 No protein-ligand interaction detected (PLIP) ACT.15: 4 residues within 4Å: Chain D: G.281, K.316 Ligands: ACT.14, ACT.16 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.316 Salt bridges: D:K.283, D:K.316 ACT.16: 4 residues within 4Å: Chain D: S.309, E.312, A.313 Ligands: ACT.15 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:E.312 Hydrogen bonds: D:S.309, D:A.313 ACT.17: 3 residues within 4Å: Chain D: M.40, D.42, F.70 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swiderek, K. et al., Modeling of isotope effects on binding oxamate to lactic dehydrogenase. J.Phys.Chem.B (2009)

Release Date

2009-09-15

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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