SMTL ID : 1ldm.1 (3 other biounits)

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: V.28, G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, L.109, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.245, I.249 Ligands: OXM.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.31, A:I.249 Hydrogen bonds: A:V.28, A:A.30, A:V.31, A:V.53, A:G.97, A:A.98, A:N.113, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:R.99, A:T.245 Salt bridges: A:R.99, A:R.99 NAD.4: 26 residues within 4Å: Chain B: V.28, G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, L.109, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.245, I.249 Ligands: OXM.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.31, B:I.249 Hydrogen bonds: B:V.28, B:A.30, B:V.31, B:V.53, B:Y.83, B:G.97, B:A.98, B:N.113, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:R.99, B:T.245 Salt bridges: B:R.99, B:R.99 NAD.7: 26 residues within 4Å: Chain C: V.28, G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, L.109, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.245, I.249 Ligands: OXM.8 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:V.31, C:I.249 Hydrogen bonds: C:V.28, C:A.30, C:V.31, C:V.53, C:Y.83, C:G.97, C:A.98, C:N.113, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:R.99, C:T.245 Salt bridges: C:R.99, C:R.99 NAD.10: 26 residues within 4Å: Chain D: V.28, G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, L.109, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.245, I.249 Ligands: OXM.11 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.31, D:I.249 Hydrogen bonds: D:V.28, D:A.30, D:V.31, D:V.53, D:G.97, D:A.98, D:N.113, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:R.99, D:T.245 Salt bridges: D:R.99, D:R.99

8 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 9 residues within 4Å: Chain A: Q.100, R.106, N.138, L.165, R.169, H.193, A.235, T.245 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.106, A:N.138, A:N.138, A:T.245 Salt bridges: A:R.106, A:R.169, A:H.193 OXM.3: 8 residues within 4Å: Chain A: R.171, H.186, W.188, V.267 Chain C: C.183, S.184, H.186, A.207 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:H.186, C:A.207 Salt bridges: C:H.186, A:R.171, A:H.186 Water bridges: A:H.186, A:H.186 OXM.5: 9 residues within 4Å: Chain B: Q.100, R.106, N.138, L.165, R.169, H.193, A.235, T.245 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.106, B:N.138, B:N.138 Salt bridges: B:R.106, B:R.169, B:H.193 OXM.6: 8 residues within 4Å: Chain B: R.171, H.186, W.188, V.267 Chain D: C.183, S.184, H.186, A.207 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Salt bridges: B:R.171, B:H.186, D:H.186 Hydrogen bonds: D:H.186, D:A.207 OXM.8: 9 residues within 4Å: Chain C: Q.100, R.106, N.138, L.165, R.169, H.193, A.235, T.245 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.106, C:N.138, C:N.138 Salt bridges: C:R.106, C:R.169, C:H.193 OXM.9: 8 residues within 4Å: Chain A: C.183, S.184, H.186, A.207 Chain C: R.171, H.186, W.188, V.267 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.186, A:A.207 Salt bridges: A:H.186, C:R.171, C:H.186 OXM.11: 9 residues within 4Å: Chain D: Q.100, R.106, N.138, L.165, R.169, H.193, A.235, T.245 Ligands: NAD.10 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.106, D:N.138, D:N.138, D:T.245 Salt bridges: D:R.106, D:R.169, D:H.193 OXM.12: 8 residues within 4Å: Chain B: C.183, S.184, H.186, A.207 Chain D: R.171, H.186, W.188, V.267 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:H.186, B:A.207 Salt bridges: B:H.186, D:R.171, D:H.186 Water bridges: D:H.186, D:H.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abad-Zapatero, C. et al., Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J.Mol.Biol. (1987)

Release Date

1989-07-12

Peptides

M4 LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

M4 LACTATE DEHYDROGENASE

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