SMTL ID : 4r4j.1

Crystal structure of complex sp_ASADH with 3-carboxypropyl-phthalic acid and Nicotinamide Adenine dinucleotide phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

2 x 3JL: 3-(3-carboxypropyl)benzene-1,2-dicarboxylic acid(Non-covalent)

3JL.1: 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.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.74, A:S.96, A:N.127, A:Q.155 Water bridges: A:S.74, A:R.245 Salt bridges: A:R.99, A:R.99, A:K.223, A:K.223, A:R.245, A:H.252 3JL.7: 15 residues within 4Å: Chain B: S.74, N.94, T.95, S.96, R.99, N.127, C.128, Q.155, G.159, I.209, E.220, K.223, R.245, H.252 Ligands: NAP.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.74, B:S.96, B:N.127, B:Q.155 Salt bridges: B:R.99, B:K.223, B:K.223, B:R.245, B:H.252

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

NAP.2: 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, R.99, P.126, N.127, C.128, S.158, G.159, G.161, M.162, G.329 Ligands: 3JL.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:V.14 Hydrogen bonds: A:G.9, A:T.11, 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:N.94, A:R.99, A:P.126, A:C.128, A:M.162 Water bridges: A:G.15, A:T.57, A:A.72, A:S.74, A:S.74, A:K.79, A:Y.80, A:Y.80, A:G.163 Salt bridges: A:R.39 NAP.8: 16 residues within 4Å: Chain B: 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 Ligands: NAP.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.39 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:S.40, B:S.40, B:T.76, B:K.79, B:K.79, B:M.162, B:G.163 Water bridges: B:V.14, B:T.57 NAP.9: 27 residues within 4Å: Chain B: G.9, A.10, T.11, G.12, A.13, V.14, A.36, S.37, S.40, S.71, A.72, G.73, T.76, N.94, T.95, R.99, P.126, N.127, C.128, S.158, G.159, G.161, M.162, G.329, A.330 Ligands: 3JL.7, NAP.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.14 Hydrogen bonds: B:G.9, B:T.11, B:T.11, B:G.12, B:A.13, B:V.14, B:S.37, B:S.37, B:S.40, B:S.40, B:T.76, B:N.94, B:R.99, B:P.126, B:N.127, B:C.128, B:M.162 Water bridges: B:G.15

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

NA.3: 5 residues within 4Å: Chain A: I.273, A.274, A.275, F.276, A.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.274, A:A.279 Water bridges: A:L.281 NA.4: 1 residues within 4Å: Chain A: E.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.343

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

EDO.5: 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.6: 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.10: 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.11: 6 residues within 4Å: Chain B: Q.17, S.250, V.297, G.298, D.324, L.326 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.250, B:G.298 EDO.12: 6 residues within 4Å: Chain B: E.282, P.291, Q.292, N.295, A.296, F.303 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.292, B:Q.292 Water bridges: B:N.295, B:N.295, B:N.295 EDO.13: 4 residues within 4Å: Chain A: T.225, K.229 Chain B: L.311, D.312 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.312 Hydrogen bonds: A:K.229

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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