SMTL ID : 4pg6.1

Crystal structure of S. aureus Homoserine Dehydrogenase at pH7.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: L.262, Y.264, D.289 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.264 Hydrogen bonds: A:L.262 Water bridges: A:K.291 Salt bridges: A:K.291 ACT.2: 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.3: 6 residues within 4Å: Chain A: V.99, M.100, G.101, A.123, N.124, K.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125 Salt bridges: A:K.125 ACT.4: 1 residues within 4Å: Chain A: D.201 No protein-ligand interaction detected (PLIP) ACT.5: 6 residues within 4Å: Chain A: L.128, V.130, H.131, I.238, K.239, L.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.240 Water bridges: A:N.241 ACT.6: 5 residues within 4Å: Chain A: Q.236, V.237, G.277, K.278, V.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.237, A:V.279 Water bridges: A:V.237 ACT.7: 4 residues within 4Å: Chain A: T.190, Q.193, N.257, D.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.193 ACT.12: 7 residues within 4Å: Chain B: V.99, M.100, G.101, A.123, N.124, K.125 Ligands: PEG.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.125 Salt bridges: B:K.125 ACT.13: 5 residues within 4Å: Chain B: K.396, A.397, L.399, P.400, F.401 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.401 ACT.14: 6 residues within 4Å: Chain B: L.128, V.130, H.131, I.238, K.239, L.240 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.128, B:V.130 Hydrogen bonds: B:L.240 ACT.15: 4 residues within 4Å: Chain B: R.46, V.58, I.59, Y.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.59 Salt bridges: B:R.46 ACT.16: 3 residues within 4Å: Chain B: G.250, D.438, K.439 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.439 ACT.17: 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: K.23, N.25, S.92, D.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.25, A:D.94 GOL.9: 2 residues within 4Å: Chain A: D.260, K.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.260, A:K.290 GOL.18: 5 residues within 4Å: Chain B: K.67, H.79, L.80, T.81, E.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.81, B:T.81 Water bridges: B:D.83

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

PEG.10: 4 residues within 4Å: Chain A: N.241, V.243, K.244, R.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:R.245 PEG.19: 6 residues within 4Å: Chain B: L.31, G.32, V.64, R.65, M.100 Ligands: ACT.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.31, B:R.65 PEG.20: 6 residues within 4Å: Chain B: H.383, V.384, K.385, H.433, G.434, Y.435 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.385, B:K.385

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 7 residues within 4Å: Chain A: G.30, L.31, G.32, V.64, R.65, R.71, M.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.31 DMS.21: 3 residues within 4Å: Chain B: L.262, D.289, R.406 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.406 Salt bridges: B:D.289 DMS.22: 4 residues within 4Å: Chain B: K.244, R.245, R.246, E.284 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.284

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

2015-05-13

Peptides

Homoserine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homoserine dehydrogenase

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