SMTL ID : 4r5h.1

Crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-carboxy-propenyl-phthalic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 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.2: 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.3: 4 residues within 4Å: Chain A: L.311, D.312 Chain B: T.225, K.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.229, B:D.235 Water bridges: B:V.239 EDO.4: 6 residues within 4Å: Chain A: E.282, P.291, Q.292, N.295, A.296, F.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.292, A:Q.292 Water bridges: A:N.295, A:N.295, A:N.295 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: 6 residues within 4Å: Chain B: Q.17, S.250, 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 EDO.11: 6 residues within 4Å: Chain B: E.282, P.291, Q.292, N.295, A.296, F.303 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.292, B:Q.292 Water bridges: B:N.295, B:N.295 EDO.12: 4 residues within 4Å: Chain A: T.225, K.229 Chain B: L.311, D.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.229

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

NA.5: 5 residues within 4Å: Chain A: I.273, A.274, A.275, F.276, A.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.279, A:A.279 NA.6: 1 residues within 4Å: Chain A: E.343 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.343

1 x 3JN: 3-[(1E)-3-carboxyprop-1-en-1-yl]benzene-1,2-dicarboxylic acid(Non-covalent)

3JN.7: 16 residues within 4Å: Chain A: S.74, N.94, T.95, S.96, R.99, N.127, C.128, Q.155, G.159, A.160, I.209, E.220, K.223, R.245, H.252 Ligands: NAP.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.74, A:S.96, A:N.127, A:Q.155 Water bridges: A:S.74, A:S.74 Salt bridges: A:R.99, A:K.223, A:K.223, A:R.245, A:H.252

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

NAP.8: 27 residues within 4Å: Chain A: G.9, A.10, T.11, G.12, A.13, V.14, A.36, S.37, R.39, S.40, T.57, S.71, A.72, G.73, T.76, N.94, T.95, C.125, P.126, N.127, C.128, S.158, G.161, M.162, G.329, A.330 Ligands: 3JN.7 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.14 Hydrogen bonds: A:G.9, A:T.11, A:T.11, A:G.12, A:A.13, A:V.14, A:S.37, A:S.37, A:R.39, A:S.40, A:S.40, A:S.40, A:N.94, A:N.94, A:C.128, A:M.162 Water bridges: A:G.15, A:A.72, A:S.74, A:S.74, A:Y.80, A:Y.80, A:G.163 Salt bridges: A:R.39 NAP.13: 17 residues within 4Å: Chain B: G.9, A.10, T.11, G.12, A.13, A.36, S.37, R.39, S.40, T.57, S.71, A.72, T.76, A.160, G.161, M.162, G.163 20 PLIP interactions: 20 interactions with chain B 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:S.40, B:S.40, B:T.76, B:M.162, B:G.163 Water bridges: B:V.14, B:V.14, B:T.57, B:Y.80

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate-semialdehyde dehydrogenase

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