SMTL ID : 1poj.3 (2 other biounits)

Isoaspartyl Dipeptidase with bound inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.2, AE1.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.68, A:H.70, A:D.285, AE1.3 ZN.2: 6 residues within 4Å: Chain A: Y.137, K.162, H.201, H.230 Ligands: ZN.1, AE1.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.201, A:H.230, AE1.3 ZN.4: 7 residues within 4Å: Chain B: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.5, AE1.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.68, B:H.70, B:D.285, AE1.6 ZN.5: 6 residues within 4Å: Chain B: Y.137, K.162, H.201, H.230 Ligands: ZN.4, AE1.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.201, B:H.230, AE1.6 ZN.7: 7 residues within 4Å: Chain C: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.8, AE1.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.68, C:H.70, C:D.285, AE1.9 ZN.8: 6 residues within 4Å: Chain C: Y.137, K.162, H.201, H.230 Ligands: ZN.7, AE1.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.201, C:H.230, AE1.9 ZN.10: 7 residues within 4Å: Chain D: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.11, AE1.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.68, D:H.70, D:D.285, AE1.12 ZN.11: 6 residues within 4Å: Chain D: Y.137, K.162, H.201, H.230 Ligands: ZN.10, AE1.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.201, D:H.230, AE1.12 ZN.13: 7 residues within 4Å: Chain E: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.14, AE1.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.68, E:H.70, E:D.285, AE1.15 ZN.14: 6 residues within 4Å: Chain E: Y.137, K.162, H.201, H.230 Ligands: ZN.13, AE1.15 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.201, E:H.230, AE1.15 ZN.16: 7 residues within 4Å: Chain F: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.17, AE1.18 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.68, F:H.70, F:D.285, AE1.18 ZN.17: 6 residues within 4Å: Chain F: Y.137, K.162, H.201, H.230 Ligands: ZN.16, AE1.18 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.201, F:H.230, AE1.18 ZN.19: 7 residues within 4Å: Chain G: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.20, AE1.21 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: G:H.68, G:H.70, G:D.285, AE1.21 ZN.20: 6 residues within 4Å: Chain G: Y.137, K.162, H.201, H.230 Ligands: ZN.19, AE1.21 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: G:H.201, G:H.230, AE1.21 ZN.22: 7 residues within 4Å: Chain H: H.68, H.70, K.162, H.230, D.285 Ligands: ZN.23, AE1.24 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:H.68, H:H.70, H:D.285, AE1.24 ZN.23: 6 residues within 4Å: Chain H: Y.137, K.162, H.201, H.230 Ligands: ZN.22, AE1.24 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:H.201, H:H.230, AE1.24

8 x AE1: 2-{[[(1S)-1-AMINO-2-CARBOXYETHYL](DIHYDROXY)PHOSPHORANYL]METHYL}-4-METHYLPENTANOIC ACID(Non-covalent)

AE1.3: 21 residues within 4Å: Chain A: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.1, ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.257, A:F.292 Hydrogen bonds: A:G.75, A:T.106, A:Y.137, A:S.289, A:S.289 Salt bridges: A:H.70, A:R.169, A:H.201, A:R.233 AE1.6: 21 residues within 4Å: Chain B: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.4, ZN.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.257, B:F.292 Hydrogen bonds: B:G.75, B:T.106, B:Y.137, B:S.289, B:S.289 Salt bridges: B:H.70, B:R.169, B:H.201, B:R.233 AE1.9: 21 residues within 4Å: Chain C: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.7, ZN.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.257, C:F.292 Hydrogen bonds: C:G.75, C:T.106, C:Y.137, C:S.289, C:S.289 Salt bridges: C:H.70, C:R.169, C:H.201, C:R.233 AE1.12: 21 residues within 4Å: Chain D: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.10, ZN.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.257, D:F.292 Hydrogen bonds: D:G.75, D:T.106, D:Y.137, D:S.289, D:S.289 Salt bridges: D:H.70, D:R.169, D:H.201, D:R.233 AE1.15: 21 residues within 4Å: Chain E: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.13, ZN.14 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.257, E:F.292 Hydrogen bonds: E:G.75, E:T.106, E:Y.137, E:S.289, E:S.289 Salt bridges: E:H.70, E:R.169, E:H.201, E:R.233 AE1.18: 21 residues within 4Å: Chain F: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.16, ZN.17 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.257, F:F.292 Hydrogen bonds: F:G.75, F:T.106, F:Y.137, F:S.289, F:S.289 Salt bridges: F:H.70, F:R.169, F:H.201, F:R.233 AE1.21: 21 residues within 4Å: Chain G: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.19, ZN.20 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:I.257, G:F.292 Hydrogen bonds: G:G.75, G:T.106, G:Y.137, G:S.289, G:S.289 Salt bridges: G:H.70, G:R.169, G:H.201, G:R.233 AE1.24: 21 residues within 4Å: Chain H: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, R.169, H.201, H.230, R.233, I.257, D.285, G.288, S.289, Q.290, P.291, F.292 Ligands: ZN.22, ZN.23 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:I.257, H:F.292 Hydrogen bonds: H:G.75, H:T.106, H:Y.137, H:S.289, H:S.289 Salt bridges: H:H.70, H:R.169, H:H.201, H:R.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jozic, D. et al., X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases. J.Mol.Biol. (2003)

Release Date

2004-06-22

Peptides

Isoaspartyl dipeptidase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
B

F
B

G
B

H
B

Isoaspartyl dipeptidase

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