SMTL ID : 1ldn.2 (1 other biounit)

STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

2 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 9 residues within 4Å: Chain A: R.157, Q.169, N.170, H.172 Chain C: R.157, Q.169, N.170, H.172, I.255 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:R.157, C:R.157, C:N.170, C:I.255, A:N.170, A:I.255 Salt bridges: C:R.157, C:H.172, C:H.172, A:R.157, A:H.172, A:H.172 FBP.4: 9 residues within 4Å: Chain B: R.157, Q.169, N.170, H.172, I.255 Chain D: R.157, Q.169, N.170, H.172 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:N.170, B:I.255, D:R.157, D:N.170, D:I.255 Salt bridges: B:R.157, B:H.172, B:H.172, D:R.157, D:H.172, D:H.172

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 8 residues within 4Å: Chain A: R.92, N.124, L.151, R.155, H.179, A.223, T.233 Ligands: NAD.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.86, A:R.92, A:N.124, A:T.233, A:T.233 Water bridges: A:T.233 Salt bridges: A:R.92, A:R.155, A:H.179 OXM.5: 9 residues within 4Å: Chain B: Q.86, R.92, N.124, L.151, R.155, H.179, A.223, T.233 Ligands: NAD.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.86, B:R.92, B:T.233, B:T.233 Water bridges: B:T.233 Salt bridges: B:R.92, B:R.155, B:H.179 OXM.7: 8 residues within 4Å: Chain C: Q.86, R.92, N.124, L.151, R.155, H.179, T.233 Ligands: NAD.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.86, C:R.92, C:T.233, C:T.233, C:T.233 Water bridges: C:T.233 Salt bridges: C:R.92, C:R.155, C:H.179 OXM.9: 8 residues within 4Å: Chain D: Q.86, R.92, N.124, R.155, H.179, A.223, T.233 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.86, D:R.92, D:T.233, D:T.233 Water bridges: D:R.92 Salt bridges: D:R.92, D:R.155, D:H.179

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

NAD.3: 24 residues within 4Å: Chain A: G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, A.84, N.85, N.99, I.102, A.122, T.123, N.124, S.147, L.151, H.179, T.233, I.237 Ligands: OXM.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.17, A:I.237, A:I.237 Hydrogen bonds: A:A.14, A:A.14, A:F.16, A:V.17, A:A.39, A:G.83, A:A.84, A:N.85, A:N.99, A:A.122, A:N.124, A:N.124, A:S.147 Water bridges: A:G.15, A:G.15, A:Q.86 NAD.6: 26 residues within 4Å: Chain B: I.12, G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, A.84, N.85, N.99, I.102, A.122, T.123, N.124, V.126, S.147, L.151, H.179, T.233, I.237 Ligands: OXM.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.237 Hydrogen bonds: B:F.16, B:V.17, B:A.39, B:N.40, B:G.83, B:N.85, B:N.99, B:A.122, B:N.124, B:S.147 Water bridges: B:G.15, B:G.18, B:Y.69, B:Y.69, B:Q.86, B:N.124 NAD.8: 23 residues within 4Å: Chain C: G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, A.84, L.95, N.99, I.102, A.122, T.123, N.124, S.147, H.179, T.233, I.237 Ligands: OXM.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:V.17, C:I.237 Hydrogen bonds: C:A.14, C:F.16, C:V.17, C:A.39, C:N.40, C:G.83, C:A.84, C:N.99, C:A.122, C:T.123, C:N.124, C:N.124, C:S.147 Water bridges: C:G.15, C:G.18 NAD.10: 27 residues within 4Å: Chain D: I.12, G.13, A.14, G.15, F.16, V.17, I.37, D.38, A.39, C.81, A.82, G.83, A.84, N.85, N.99, I.102, I.106, A.122, T.123, N.124, V.126, S.147, L.151, H.179, T.233, I.237 Ligands: OXM.9 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:V.17, D:I.237 Hydrogen bonds: D:A.14, D:F.16, D:V.17, D:A.39, D:G.83, D:A.84, D:N.99, D:A.122, D:N.124, D:N.124, D:S.147 Water bridges: D:G.15, D:G.18, D:Y.69, D:Y.69, D:Q.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wigley, D.B. et al., Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution. J.Mol.Biol. (1992)

Release Date

1994-01-31

Peptides

L-LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

L-LACTATE DEHYDROGENASE

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