SMTL ID : 4pg7.1

Crystal structure of S. aureus Homoserine Dehydrogenase at pH7.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

11 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: V.99, M.100, G.101, A.123, N.124, K.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.125 ACT.2: 1 residues within 4Å: Chain A: D.201 No protein-ligand interaction detected (PLIP) ACT.3: 4 residues within 4Å: Chain A: Y.301, Y.317 Chain B: Y.305, D.313 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.301 Hydrogen bonds: A:Y.317, B:D.313 ACT.4: 4 residues within 4Å: Chain A: L.262, G.263, Y.264, D.289 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.264 Hydrogen bonds: A:L.262 Salt bridges: A:K.291, A:R.406 ACT.5: 4 residues within 4Å: Chain A: K.244, R.245, R.246, E.284 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.246 Salt bridges: A:R.246 ACT.10: 6 residues within 4Å: Chain B: V.99, M.100, G.101, A.123, N.124, K.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.125 ACT.11: 5 residues within 4Å: Chain B: L.262, Y.264, D.289, R.406 Ligands: ACT.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.289 Water bridges: B:Y.264, B:K.291, B:K.291 Salt bridges: B:K.291, B:R.406 ACT.12: 4 residues within 4Å: Chain B: D.260, Q.261, G.263, K.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.261 Salt bridges: B:K.290 ACT.13: 5 residues within 4Å: Chain B: Y.264, R.406, V.418, V.420 Ligands: ACT.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.264, B:V.418 Water bridges: B:S.404, B:S.404, B:R.406 Salt bridges: B:R.406 ACT.16: 4 residues within 4Å: Chain B: A.397, L.399, P.400, F.401 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.401 Water bridges: B:L.399 ACT.17: 4 residues within 4Å: Chain B: R.46, V.58, I.59, Y.78 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.78 Salt bridges: B:R.46

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: D.260, K.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.290, A:K.290 GOL.7: 4 residues within 4Å: Chain A: K.23, N.25, S.92, D.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.25, A:N.25, A:S.92 GOL.8: 5 residues within 4Å: Chain A: K.67, H.79, L.80, T.81, E.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.81 Water bridges: A:E.82 GOL.18: 3 residues within 4Å: Chain B: K.67, H.79, L.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.80

1 x LYS: LYSINE(Non-covalent)

LYS.9: 5 residues within 4Å: Chain A: R.246, G.250, T.252, D.438, K.439 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:K.439 Hydrogen bonds: A:R.246, K.9, K.9 Water bridges: A:G.250 Salt bridges: A:K.439

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 4 residues within 4Å: Chain B: H.383, H.433, G.434, Y.435 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.383 Water bridges: B:K.385, B:Y.435, B:Y.435 PEG.15: 3 residues within 4Å: Chain B: N.235, Q.236, V.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.235, B:V.237 Water bridges: B:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Navratna, V. et al., Structural basis for the catalytic mechanism of homoserine dehydrogenase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-05-06

Peptides

Homoserine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homoserine dehydrogenase

Related Entries With Identical Sequence