SMTL ID : 3vph.1

L-lactate dehydrogenase from Thermus caldophilus GK24 complexed with oxamate, NADH and FBP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.1: 7 residues within 4Å: Chain A: N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.117, A:T.227, A:T.227, A:T.227 Water bridges: A:A.217, A:T.227 Salt bridges: A:R.148, A:H.172 OXM.5: 7 residues within 4Å: Chain B: N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.117, B:T.227, B:T.227 Salt bridges: B:R.148, B:H.172 OXM.9: 6 residues within 4Å: Chain C: N.117, L.144, R.148, H.172, A.217, T.227 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.117, C:T.227, C:T.227 Water bridges: C:A.217, C:T.227, C:T.227 Salt bridges: C:R.148, C:H.172 OXM.11: 7 residues within 4Å: Chain D: N.117, L.144, R.148, H.172, A.217, T.227 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.117, D:T.227 Salt bridges: D:R.148, D:H.172

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

FBP.2: 11 residues within 4Å: Chain A: R.150, Q.162, H.165, Y.167 Chain D: R.150, Q.162, S.163, H.165, Y.167 Ligands: GOL.4, GOL.13 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain A Water bridges: D:Y.167, D:Y.167, D:Y.167, D:V.249 Salt bridges: D:R.150, D:H.165, D:H.165, A:R.150, A:H.165, A:H.165 Hydrogen bonds: A:R.150, A:Q.162, A:Q.162, A:Y.167, A:Y.167, A:Y.167 FBP.6: 11 residues within 4Å: Chain B: R.150, Q.162, H.165, Y.167 Chain C: R.150, Q.162, H.165, Y.167, V.249 Ligands: GOL.8, GOL.10 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:Q.162, B:Y.167, C:R.150, C:Y.167, C:Y.167 Water bridges: B:V.249, C:P.161, C:Y.167 Salt bridges: B:R.150, B:H.165, B:H.165, C:R.150, C:H.165, C:H.165

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

NAD.3: 24 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.95, V.99, A.115, T.116, N.117, S.140, L.144, H.172, T.227, I.231 Ligands: OXM.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.11, A:I.231, A:I.231, A:I.231 Hydrogen bonds: A:M.10, A:V.11, A:L.33, A:Y.62, A:Y.62, A:G.76, A:A.115, A:N.117, A:N.117, A:S.140 Water bridges: A:G.9, A:G.12 NAD.7: 22 residues within 4Å: Chain B: 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, S.140, H.172, T.227, I.231 Ligands: OXM.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.11, B:I.231, B:I.231 Hydrogen bonds: B:M.10, B:V.11, B:G.12, B:L.33, B:Y.62, B:G.76, B:N.117, B:N.117, B:S.140, B:S.140 Water bridges: B:G.9, B:D.34, B:N.92, B:N.92, B:N.92 NAD.12: 23 residues within 4Å: Chain D: 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.95, V.99, A.115, T.116, N.117, S.140, H.172, T.227, I.231 Ligands: OXM.11 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.11, D:I.231, D:I.231, D:I.231 Hydrogen bonds: D:M.10, D:V.11, D:L.33, D:Y.62, D:Y.62, D:G.76, D:A.115, D:N.117, D:S.140 Water bridges: D:G.9, D:G.9

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: I.143, T.146, A.147, R.150, Q.162, Y.250 Chain B: P.50, F.51 Ligands: FBP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.143, A:R.150 Water bridges: A:V.249 GOL.8: 9 residues within 4Å: Chain A: P.50, F.51 Chain B: I.143, T.146, A.147, R.150, Q.162, Y.250 Ligands: FBP.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.143, B:A.147, B:R.150, B:Q.162 GOL.10: 7 residues within 4Å: Chain C: I.143, T.146, A.147, R.150, Y.250 Chain D: F.51 Ligands: FBP.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.143, C:A.147 Water bridges: C:R.150, C:R.150 GOL.13: 7 residues within 4Å: Chain C: P.50, F.51 Chain D: I.143, T.146, A.147, R.150 Ligands: FBP.2 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.143, D:A.147, D:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikehara, Y. et al., The core of allosteric motion in Thermus caldophilus L-lactate dehydrogenase. J.Biol.Chem. (2014)

Release Date

2013-03-06

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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