SMTL ID : 5x9d.1

Crystal structure of homoserine dehydrogenase in complex with L-cysteine and NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 80F: (2R)-3-[[(4S)-3-aminocarbonyl-1-[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4H-pyridin-4-yl]sulfanyl]-2-azanyl-propanoic acid(Non-covalent)

80F.1: 35 residues within 4Å: Chain A: F.6, G.7, Y.8, G.9, N.10, V.11, T.37, R.38, V.72, S.73, S.74, A.75, P.82, T.100, N.101, K.102, G.127, S.131, N.155, G.156, T.157, G.182, Y.183, A.184, E.185, E.186, D.191, D.196, K.200, G.282, A.283, G.284, P.285, A.288 Ligands: TLA.2 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:Y.8, A:Y.8, A:V.11, A:R.38, A:R.38, A:S.73, A:S.74, A:G.156, A:T.157, A:T.157, A:T.157, A:G.182, A:E.185, A:E.185, A:E.185, A:D.191, A:G.284 Water bridges: A:G.9, A:G.9, A:N.10, A:N.10, A:N.10, A:T.37, A:R.38, A:R.38, A:A.75, A:A.75, A:K.102, A:A.184, A:E.186, A:E.186, A:K.200 Salt bridges: A:K.200 pi-Stacking: A:F.6 80F.3: 35 residues within 4Å: Chain B: F.6, G.7, Y.8, G.9, N.10, V.11, T.37, R.38, V.72, S.73, S.74, A.75, P.82, T.100, N.101, K.102, G.127, S.131, N.155, G.156, T.157, G.182, Y.183, A.184, E.185, E.186, D.191, D.196, K.200, G.282, A.283, G.284, P.285, A.288 Ligands: TLA.4 34 PLIP interactions: 34 interactions with chain B Hydrogen bonds: B:Y.8, B:Y.8, B:V.11, B:R.38, B:R.38, B:S.73, B:S.74, B:G.156, B:T.157, B:T.157, B:T.157, B:G.182, B:E.185, B:E.185, B:E.185, B:D.191, B:G.284 Water bridges: B:G.9, B:G.9, B:N.10, B:N.10, B:N.10, B:T.37, B:R.38, B:R.38, B:A.75, B:A.75, B:K.102, B:A.184, B:E.186, B:E.186, B:K.200 Salt bridges: B:K.200 pi-Stacking: B:F.6

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 4 residues within 4Å: Chain A: T.37, R.38, R.39 Ligands: 80F.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.37, A:T.37, A:R.38, A:R.39 Salt bridges: A:R.38, A:R.39 TLA.4: 4 residues within 4Å: Chain B: T.37, R.38, R.39 Ligands: 80F.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.37, B:T.37, B:R.38, B:R.39 Salt bridges: B:R.38, B:R.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogata, K. et al., Inhibition of homoserine dehydrogenase by formation of a cysteine-NAD covalent complex. Sci Rep (2018)

Release Date

2018-05-02

Peptides

Homoserine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Homoserine dehydrogenase

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