SMTL ID : 1pok.4 (3 other biounits)

Crystal structure of Isoaspartyl Dipeptidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 10 residues within 4Å: Chain A: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, G.288, S.289 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.75, A:T.106, A:T.106, A:S.289 Water bridges: A:G.75, A:G.105, A:T.106 Salt bridges: A:H.70 SO4.5: 10 residues within 4Å: Chain B: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, S.289 Ligands: ZN.6, ASN.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.75, B:E.77, B:E.77, B:T.106 Water bridges: B:H.70, B:L.103 Salt bridges: B:H.70

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.68, H.70, K.162, D.285 Ligands: SO4.1, ZN.3, ASN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.68, A:H.70, A:D.285 ZN.3: 8 residues within 4Å: Chain A: H.68, Y.137, K.162, H.201, H.230, D.285 Ligands: ZN.2, ASN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.201 ZN.6: 7 residues within 4Å: Chain B: H.68, H.70, K.162, D.285 Ligands: SO4.5, ZN.7, ASN.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.70, B:D.285 ZN.7: 7 residues within 4Å: Chain B: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.6, ASN.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.201, ASN.8

2 x ASN: ASPARAGINE(Non-covalent)

ASN.4: 8 residues within 4Å: Chain A: Y.137, R.169, H.201, H.230, R.233, D.285 Ligands: ZN.2, ZN.3 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:Y.137, A:R.169, A:R.169, A:R.233, N.4, N.4, N.4 Salt bridges: A:H.201, A:H.230 ASN.8: 10 residues within 4Å: Chain B: Y.137, R.169, H.201, H.230, R.233, D.285, S.289 Ligands: SO4.5, ZN.6, ZN.7 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:Y.137, B:R.169, B:R.169, B:R.169, B:H.201, B:R.233, B:R.233, B:S.289, B:S.289, N.8 Salt bridges: B:H.230

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoaspartyl dipeptidase

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