SMTL ID : 3q11.1

Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase from Streptococcus pneumoniae with NADP and aspartyl beta-difluorophosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 15 residues within 4Å: Chain A: G.9, T.11, G.12, A.13, A.36, S.37, R.39, S.40, T.57, S.71, A.72, T.76, G.161, M.162, G.163 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.9, A:T.11, A:T.11, A:T.11, A:T.11, A:G.12, A:A.13, A:S.37, A:S.37, A:R.39, A:S.40, A:S.40, A:M.162, A:G.163 Water bridges: A:V.14, A:V.14, A:T.57, A:Y.80, A:A.160, A:A.164 Salt bridges: A:R.39 NAP.7: 16 residues within 4Å: Chain B: G.9, T.11, G.12, A.13, A.36, S.37, R.39, S.40, T.57, A.72, T.76, A.160, G.161, M.162, G.163, L.166 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:M.162 Hydrogen bonds: B:G.9, B:T.11, B:T.11, B:T.11, B:G.12, B:A.13, B:S.37, B:S.37, B:R.39, B:S.40, B:S.40, B:T.76, B:M.162, B:G.163 Water bridges: B:V.14, B:V.14, B:A.164 Salt bridges: B:R.39

2 x P4F: 5,5-difluoro-4-oxo-5-phosphono-D-norvaline(Non-covalent)

P4F.2: 12 residues within 4Å: Chain A: N.94, R.99, N.127, C.128, Q.155, G.159, I.209, D.210, E.220, K.223, R.245, H.252 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.94, A:R.99, A:R.99, A:N.127, A:C.128, A:G.159, A:D.210, A:K.223, A:R.245 Water bridges: A:N.94, A:S.96, A:P.126, A:N.325 Salt bridges: A:R.245, A:H.252 P4F.8: 10 residues within 4Å: Chain B: R.99, N.127, C.128, Q.155, G.159, I.209, E.220, K.223, R.245, H.252 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.99, B:R.99, B:N.127, B:C.128, B:Q.155, B:G.159, B:E.220, B:K.223, B:R.245 Water bridges: B:N.94, B:N.94, B:N.94, B:P.126 Salt bridges: B:R.245, B:H.252

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

NA.3: 1 residues within 4Å: Chain A: E.343 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: E.24, S.25, W.332, E.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:E.339 EDO.5: 7 residues within 4Å: Chain A: Q.17, S.250, V.297, G.298, D.324, L.326, L.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.250, A:G.298 EDO.6: 4 residues within 4Å: Chain A: L.311, D.312 Chain B: T.225, K.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.229 EDO.9: 4 residues within 4Å: Chain B: E.24, S.25, W.332, E.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.24 Water bridges: B:E.339, B:E.339 EDO.10: 7 residues within 4Å: Chain B: Q.17, S.250, V.297, G.298, D.324, L.326, L.327 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.250, B:G.298 Water bridges: B:Q.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pavlovsky, A.G. et al., Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family. Chem.Biol.Drug Des. (2012)

Release Date

2012-01-04

Peptides

Aspartate-semialdehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate-semialdehyde dehydrogenase

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