SMTL ID : 3h3j.1

Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: I.12, G.15, A.16, V.17, D.38, L.39, Y.69, C.81, A.82, G.83, A.84, R.85, L.95, N.99, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.17, A:V.236, A:V.236 Hydrogen bonds: A:A.16, A:V.17, A:L.39, A:G.83, A:A.84, A:N.99, A:A.122, A:N.124, A:N.124, A:S.147 Water bridges: A:G.15, A:G.18, A:Y.69, A:R.85, A:Q.86, A:S.105 Salt bridges: A:R.85, A:R.85 NAD.4: 25 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, R.85, L.95, N.99, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.5 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:V.17, B:V.236, B:V.236 Hydrogen bonds: B:N.14, B:A.16, B:V.17, B:L.39, B:G.83, B:A.84, B:N.99, B:A.122, B:N.124, B:N.124, B:S.147 Water bridges: B:G.15, B:G.18, B:Y.69, B:R.85, B:Q.86, B:S.105 Salt bridges: B:R.85, B:R.85 NAD.7: 25 residues within 4Å: Chain C: I.12, G.15, A.16, V.17, D.38, L.39, Y.69, C.81, A.82, G.83, A.84, R.85, L.95, N.99, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.8 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:V.17, C:V.236, C:V.236 Hydrogen bonds: C:A.16, C:V.17, C:L.39, C:Y.69, C:G.83, C:A.84, C:N.99, C:A.122, C:N.124, C:N.124, C:S.147 Water bridges: C:G.15, C:G.18, C:Y.69, C:R.85, C:Q.86, C:S.105 Salt bridges: C:R.85, C:R.85 NAD.10: 25 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, R.85, L.95, N.99, I.102, I.106, A.122, T.123, N.124, S.147, L.151, H.179, T.232, V.236 Ligands: PYR.11 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:V.17, D:V.236, D:V.236 Hydrogen bonds: D:N.14, D:A.16, D:V.17, D:L.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:R.85, D:Q.86, D:S.105 Salt bridges: D:R.85, D:R.85

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: Q.86, R.92, N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.92, A:N.124 Water bridges: A:T.232 Salt bridges: A:R.92, A:R.155, A:H.179 PYR.5: 9 residues within 4Å: Chain B: Q.86, R.92, N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.222 Hydrogen bonds: B:R.92, B:N.124, B:T.232 Water bridges: B:R.92, B:T.232 Salt bridges: B:R.92, B:R.155, B:H.179 PYR.8: 9 residues within 4Å: Chain C: Q.86, R.92, N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.92, C:N.124, C:T.232 Salt bridges: C:R.92, C:R.155, C:H.179 PYR.11: 9 residues within 4Å: Chain D: Q.86, R.92, N.124, L.151, R.155, H.179, A.222, T.232 Ligands: NAD.10 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.222 Hydrogen bonds: D:R.92, D:N.124, D:T.232, D:T.232 Water bridges: D:R.92 Salt bridges: D:R.92, D:R.155, D:H.179

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.188, H.189, N.191, G.194 Chain B: S.188, H.189, N.191, G.194 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.194, B:S.188 GOL.6: 7 residues within 4Å: Chain A: V.277, R.284, N.285, V.287 Chain B: F.164, V.166, Q.195 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.284, A:N.285, A:N.285, B:Q.195, B:Q.195 Water bridges: A:E.288 GOL.9: 8 residues within 4Å: Chain C: S.188, H.189, N.191, G.194 Chain D: S.188, H.189, N.191, G.194 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:S.188, C:G.194 GOL.12: 7 residues within 4Å: Chain C: V.277, R.284, N.285, V.287 Chain D: F.164, V.166, Q.195 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Q.195, D:Q.195, C:R.284, C:N.285, C:N.285 Water bridges: C:E.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, M.-C. et al., Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate. To be Published

Release Date

2010-04-28

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