SMTL ID : 4r5m.1

Crystal structure of Vc-Aspartate beta-semialdehyde-dehydrogenase with NADP and 4-Nitro-2-Phosphono-Benzoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: G.210, F.212, T.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.212, A:T.214

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

NAP.2: 15 residues within 4Å: Chain A: G.7, R.9, G.10, M.11, V.12, S.35, T.36, S.37, C.71, Q.72, G.73, S.164, G.165, Q.350 Ligands: 4NO.3 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.7, A:R.9, A:G.10, A:M.11, A:V.12, A:T.36, A:T.36, A:Q.72, A:Q.350 Water bridges: A:G.7, A:G.7, A:G.13, A:F.34, A:Q.72, B:S.194 Salt bridges: A:R.9 pi-Cation interactions: A:R.9, A:R.9 NAP.4: 14 residues within 4Å: Chain A: P.192 Chain B: G.7, R.9, G.10, M.11, V.12, S.35, T.36, S.37, C.71, Q.72, G.73, G.165 Ligands: 4NO.5 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.7, B:R.9, B:G.10, B:M.11, B:V.12, B:T.36, B:S.37, B:Q.72, B:Q.72, A:P.192 Water bridges: B:W.8, B:R.9, B:G.13, B:F.34, B:S.37, B:S.37, B:Q.72, B:G.74 Salt bridges: B:R.9 pi-Cation interactions: B:R.9, B:R.9

2 x 4NO: 4-nitro-2-phosphonobenzoic acid(Non-covalent)

4NO.3: 11 residues within 4Å: Chain A: V.12, C.71, G.73, G.74, A.96, A.97, S.98, R.101, N.133, K.243 Ligands: NAP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.97 Hydrogen bonds: A:G.74, A:S.98, A:S.98, A:T.99, A:N.133 Water bridges: A:S.98, A:T.99, A:K.243 Salt bridges: A:R.101, A:K.243 4NO.5: 10 residues within 4Å: Chain B: V.12, C.71, G.73, G.74, A.96, A.97, S.98, R.101, N.133 Ligands: NAP.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.74, B:S.98, B:S.98, B:T.99 Water bridges: B:N.133 Salt bridges: B:R.101, B:K.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pavlovsky, A.G. et al., A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-12-10

Peptides

Aspartate-semialdehyde dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate-semialdehyde dehydrogenase 1