SMTL ID : 3d4p.1 (2 other biounits)

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: I.12, G.15, A.16, V.17, D.38, L.39, C.81, A.82, G.83, A.84, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.17, A:V.236 Hydrogen bonds: A:A.16, A:V.17, A:L.39, A:G.83, A:G.83, A:A.85, A:N.124, A:N.124, A:S.147 Water bridges: A:G.15, A:G.18, A:Q.86, A:Q.86, A:H.179 NAD.3: 23 residues within 4Å: Chain B: I.12, N.14, G.15, A.16, V.17, D.38, L.39, C.81, A.82, G.83, A.84, A.85, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.17, B:V.236, B:V.236 Hydrogen bonds: B:A.16, B:V.17, B:L.39, B:G.83, B:G.83, B:A.85, B:N.124, B:N.124, B:S.147 Water bridges: B:G.15, B:G.18, B:Q.86, B:Q.86, B:H.179 NAD.5: 21 residues within 4Å: Chain C: I.12, G.15, A.16, V.17, D.38, L.39, C.81, A.82, G.83, A.84, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.6 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:V.17, C:V.236 Hydrogen bonds: C:A.16, C:V.17, C:L.39, C:G.83, C:G.83, C:A.85, C:N.124, C:N.124, C:S.147 Water bridges: C:G.15, C:G.18, C:Y.69, C:Q.86, C:Q.86, C:H.179 NAD.7: 23 residues within 4Å: Chain D: I.12, N.14, G.15, A.16, V.17, D.38, L.39, C.81, A.82, G.83, A.84, A.85, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.8 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:V.17, D:V.236, D:V.236 Hydrogen bonds: D:A.16, D:V.17, D:L.39, D:G.83, D:G.83, D:A.85, D:N.124, D:N.124, D:S.147 Water bridges: D:G.15, D:G.18, D:Y.69, D:Q.86, D:Q.86, D:H.179

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 7 residues within 4Å: Chain A: N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.222 Hydrogen bonds: A:N.124, A:T.232 Salt bridges: A:R.155, A:H.179 PYR.4: 7 residues within 4Å: Chain B: N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.222 Hydrogen bonds: B:N.124, B:T.232, B:T.232 Salt bridges: B:R.155, B:H.179 PYR.6: 7 residues within 4Å: Chain C: N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.222 Hydrogen bonds: C:N.124 Water bridges: C:T.232 Salt bridges: C:R.155, C:H.179 PYR.8: 7 residues within 4Å: Chain D: N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.222 Hydrogen bonds: D:N.124, D:T.232 Water bridges: D:T.232 Salt bridges: D:R.155, D:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schramm, V.L. et al., Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate. To be Published

Release Date

2009-06-02

Peptides

L-lactate dehydrogenase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lactate dehydrogenase 1

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