SMTL ID : 7f4c.1

The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon Sulfurisphaera tokodaii.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 27 residues within 4Å: Chain A: F.6, G.7, Y.8, G.9, N.10, V.11, T.37, R.38, R.39, V.72, S.73, S.74, A.75, T.100, N.101, K.102, G.127, S.131, G.182, Y.183, E.185, E.186, A.283, G.284, P.285, A.288 Ligands: BU1.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.11, A:A.288 Hydrogen bonds: A:Y.8, A:Y.8, A:G.9, A:N.10, A:V.11, A:T.37, A:R.38, A:R.39, A:S.73, A:S.74, A:A.75, A:G.182, A:E.185, A:G.284 Water bridges: A:G.12, A:E.186 Salt bridges: A:R.38, A:R.39 pi-Stacking: A:F.6 NAP.3: 26 residues within 4Å: Chain B: F.6, G.7, Y.8, G.9, N.10, V.11, T.37, R.38, R.39, V.72, S.73, S.74, A.75, T.100, N.101, K.102, G.127, S.131, G.182, E.185, E.186, A.283, G.284, P.285, A.288 Ligands: BU1.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.288 Hydrogen bonds: B:Y.8, B:Y.8, B:G.9, B:N.10, B:V.11, B:T.37, B:R.38, B:R.39, B:S.73, B:S.74, B:A.75, B:T.100, B:G.182, B:E.185, B:G.284 Water bridges: B:G.12, B:E.186, B:E.186 Salt bridges: B:R.38 pi-Stacking: B:F.6

2 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.2: 13 residues within 4Å: Chain A: K.102, S.131, N.155, G.156, T.157, Y.183, E.185, D.191, D.196, K.200, G.282, A.283 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.283 Hydrogen bonds: A:K.102, A:G.156, A:K.200 Water bridges: A:T.128, A:M.130, A:S.131, A:K.200 BU1.4: 12 residues within 4Å: Chain B: K.102, N.155, G.156, T.157, Y.183, E.185, D.191, D.196, K.200, G.282, A.283 Ligands: NAP.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.283 Hydrogen bonds: B:K.102, B:N.155, B:G.156, B:T.157, B:K.200 Water bridges: B:T.128, B:M.130, B:S.131, B:K.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubota, T. et al., Conformational changes in the catalytic region are responsible for heat-induced activation of hyperthermophilic homoserine dehydrogenase. Commun Biol (2022)

Release Date

2022-06-22

Peptides

Homoserine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homoserine dehydrogenase

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