SMTL ID : 4xb2.1

Hyperthermophilic archaeal homoserine dehydrogenase mutant in complex with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 21 residues within 4Å: Chain A: F.24, G.25, F.26, G.27, T.28, V.29, D.55, R.56, V.107, S.108, S.109, W.110, S.130, N.131, K.132, S.157, G.310, G.311, G.312, T.316 Ligands: HSE.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.316 Hydrogen bonds: A:F.26, A:F.26, A:T.28, A:V.29, A:R.56, A:R.56, A:S.108, A:S.109, A:S.109, A:G.312 Water bridges: A:G.27, A:G.30, A:K.132 Salt bridges: A:R.56 pi-Cation interactions: A:R.56 NDP.4: 20 residues within 4Å: Chain B: F.24, G.25, F.26, G.27, T.28, V.29, D.55, R.56, V.107, S.108, S.109, W.110, S.130, N.131, K.132, S.157, G.311, G.312, T.316 Ligands: HSE.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.316 Hydrogen bonds: B:F.26, B:F.26, B:T.28, B:V.29, B:R.56, B:S.108, B:S.109, B:K.132, B:G.312 Water bridges: B:G.27, B:T.28, B:T.28, B:G.30, B:D.55, B:R.56, B:R.56, B:N.131, B:K.221, B:K.221 Salt bridges: B:R.56

2 x HSE: L-HOMOSERINE(Non-covalent)

HSE.2: 9 residues within 4Å: Chain A: K.132, V.185, N.186, A.187, S.188, D.222, K.231, G.310 Ligands: NDP.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.132, A:K.132, A:N.186, A:A.187, A:S.188, A:K.231, A:N.292, A:G.310 Water bridges: A:G.310 HSE.5: 8 residues within 4Å: Chain B: K.132, V.185, N.186, D.222, D.227, K.231, G.310 Ligands: NDP.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.186, B:K.231, B:G.310 Water bridges: B:K.132, B:K.132, B:A.187, B:A.187, B:S.188, B:S.188 Salt bridges: B:K.231

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: E.156, V.159, M.160, A.161, T.163, I.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.156, A:I.165 NA.6: 6 residues within 4Å: Chain B: E.156, V.159, M.160, A.161, T.163, I.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayashi, J. et al., Crystal Structures of a Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest a Novel Cofactor Binding Mode for Oxidoreductases. Sci Rep (2015)

Release Date

2015-07-15

Peptides

319aa long hypothetical homoserine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

319aa long hypothetical homoserine dehydrogenase