SMTL ID : 2v7p.1

Crystal structure of lactate dehydrogenase from Thermus Thermophilus HB8 (Holo form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.1: 9 residues within 4Å: Chain A: Q.79, R.85, N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.79, A:R.85, A:N.117, A:N.117 Salt bridges: A:R.85, A:R.148, A:H.172 OXM.3: 7 residues within 4Å: Chain B: N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.117, B:T.227, B:T.227, B:T.227 Salt bridges: B:R.148, B:H.172 OXM.5: 9 residues within 4Å: Chain C: Q.79, R.85, N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.79, C:R.85, C:N.117, C:N.117 Water bridges: C:T.227 Salt bridges: C:R.85, C:R.148, C:H.172 OXM.7: 7 residues within 4Å: Chain D: N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.117, D:N.117, D:T.227, D:T.227 Water bridges: D:T.227 Salt bridges: D:R.148, D:H.172

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

NAD.2: 29 residues within 4Å: Chain A: V.6, G.7, G.9, M.10, V.11, V.31, D.32, L.33, L.37, Y.62, A.74, A.75, G.76, V.77, A.78, Q.79, N.92, V.95, V.99, A.115, T.116, N.117, V.119, S.140, L.144, H.172, T.227, I.231 Ligands: OXM.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.231, A:I.231 Hydrogen bonds: A:M.10, A:V.11, A:L.33, A:Y.62, A:G.76, A:G.76, A:V.77, A:N.92, A:N.117, A:S.140, A:S.140 Water bridges: A:G.9, A:G.12 NAD.4: 22 residues within 4Å: Chain B: V.6, G.7, G.9, M.10, V.11, D.32, L.33, L.37, A.74, A.75, V.95, V.99, A.115, T.116, N.117, V.119, S.140, L.144, H.172, T.227, I.231 Ligands: OXM.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.231 Hydrogen bonds: B:M.10, B:V.11, B:L.33, B:N.117, B:N.117, B:S.140, B:S.140 Water bridges: B:G.9, B:G.12, B:Y.62 NAD.6: 25 residues within 4Å: Chain C: G.7, G.9, M.10, V.11, D.32, L.33, L.37, Y.62, A.74, A.75, G.76, V.77, A.78, N.92, V.95, V.99, A.115, T.116, N.117, V.119, S.140, H.172, T.227, I.231 Ligands: OXM.5 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.11, C:I.231, C:I.231, C:I.231 Hydrogen bonds: C:M.10, C:V.11, C:L.33, C:Y.62, C:Y.62, C:G.76, C:N.92, C:N.117, C:N.117, C:S.140 Water bridges: C:G.9, C:G.12, C:Q.79, C:S.140, C:H.172 NAD.8: 24 residues within 4Å: Chain D: V.6, G.7, G.9, M.10, V.11, D.32, L.33, L.37, Y.62, A.74, A.75, G.76, V.95, V.99, A.115, T.116, N.117, V.119, S.140, L.144, H.172, T.227, I.231 Ligands: OXM.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.231 Hydrogen bonds: D:M.10, D:V.11, D:L.33, D:G.76, D:N.117, D:N.117, D:S.140 Water bridges: D:G.9, D:G.12, D:S.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coquelle, N. et al., Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments. J. Mol. Biol. (2007)

Release Date

2007-09-25

Peptides

L-LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-LACTATE DEHYDROGENASE

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