SMTL ID : 4r41.1

Complex Crystal structure of 4-nitro-2-phosphono-benzoic acid with sp-Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-dinucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

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

4NO.1: 11 residues within 4Å: Chain A: V.14, S.71, A.72, G.73, S.74, N.94, T.95, S.96, R.99, N.127, K.223 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.95 Hydrogen bonds: A:S.74, A:S.74, A:S.74, A:S.96, A:N.127 Salt bridges: A:R.99, A:K.223 4NO.11: 11 residues within 4Å: Chain B: V.14, S.71, A.72, G.73, S.74, N.94, T.95, S.96, R.99, N.127, K.223 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.95 Hydrogen bonds: B:S.74, B:S.74, B:S.96, B:N.127 Salt bridges: B:R.99, B:K.223

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

NAP.2: 17 residues within 4Å: Chain A: G.9, A.10, T.11, G.12, A.13, A.36, S.37, R.39, S.40, T.57, A.72, T.76, K.79, G.161, M.162, G.163, L.166 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.166 Hydrogen bonds: A:G.9, A:T.11, A:T.11, A:T.11, A:T.11, A:A.13, A:S.37, A:S.37, A:R.39, A:S.40, A:S.40, A:K.79, A:K.79, A:M.162, A:G.163 Water bridges: A:V.14, A:T.57, A:Y.80, A:A.164 Salt bridges: A:R.39 NAP.12: 16 residues within 4Å: Chain B: G.9, A.10, T.11, G.12, A.13, A.36, S.37, R.39, S.40, K.43, T.57, A.72, T.76, G.161, M.162, G.163 19 PLIP interactions: 19 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:S.40, B:S.40, B:S.40, B:K.43, B:T.76, B:M.162, B:G.163 Water bridges: B:V.14, B:T.57, B:K.79, B:Y.80

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: V.111, H.114, R.141, I.231, M.232, E.233 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.114, A:R.141

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

NA.4: 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:G.278 NA.5: 1 residues within 4Å: Chain A: E.343 No protein-ligand interaction detected (PLIP) NA.13: 3 residues within 4Å: Chain B: D.147, S.236, A.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.147, B:A.238

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

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.7: 6 residues within 4Å: Chain A: E.282, P.291, Q.292, N.295, A.296, F.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.292, A:Q.292 Water bridges: A:N.295 EDO.8: 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 EDO.9: 5 residues within 4Å: Chain A: E.24, S.25, T.26, W.332, E.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24, A:T.26 EDO.10: 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.14: 7 residues within 4Å: Chain B: Q.17, S.250, V.297, G.298, D.324, L.326, L.327 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.250, B:G.298 EDO.15: 6 residues within 4Å: Chain B: E.282, P.291, Q.292, N.295, A.296, F.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.290, B:Q.292, B:N.295 EDO.16: 5 residues within 4Å: Chain A: D.312, A.313 Chain B: D.147, R.148, A.238 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.312, B:D.147 Water bridges: A:E.314

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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