SMTL ID : 1onx.1

Crystal structure of isoaspartyl dipeptidase from escherichia coli complexed with aspartate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

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

8 x ASP: ASPARTIC ACID(Non-covalent)

ASP.3: 15 residues within 4Å: Chain A: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, D.285, G.288, S.289, P.291 Ligands: ZN.1, ZN.2 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.137 Hydrogen bonds: A:G.75, A:T.106, A:R.169, A:S.289, A:S.289, D.3 Water bridges: A:D.107 Salt bridges: A:H.70, A:H.70, A:H.201, A:H.230 ASP.6: 16 residues within 4Å: Chain B: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, H.230, D.285, G.288, S.289, P.291 Ligands: ZN.4, ZN.5 17 PLIP interactions: 14 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.137 Hydrogen bonds: B:G.75, B:T.106, B:T.106, B:Y.137, B:S.289, B:S.289, B:S.289, D.6, D.6, D.6 Water bridges: B:R.169, B:R.169 Salt bridges: B:H.70, B:H.70, B:H.201, B:H.230 ASP.9: 15 residues within 4Å: Chain C: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, D.285, G.288, S.289, P.291 Ligands: ZN.7, ZN.8 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.137 Hydrogen bonds: C:G.75, C:T.106, C:R.169, C:S.289, C:S.289, D.9 Water bridges: C:D.107 Salt bridges: C:H.70, C:H.70, C:H.201, C:H.230 ASP.12: 16 residues within 4Å: Chain D: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, H.230, D.285, G.288, S.289, P.291 Ligands: ZN.10, ZN.11 17 PLIP interactions: 14 interactions with chain D, 3 Ligand-Ligand interactions Hydrophobic interactions: D:Y.137 Hydrogen bonds: D:G.75, D:T.106, D:T.106, D:Y.137, D:S.289, D:S.289, D:S.289, D.12, D.12, D.12 Water bridges: D:R.169, D:R.169 Salt bridges: D:H.70, D:H.70, D:H.201, D:H.230 ASP.15: 15 residues within 4Å: Chain E: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, D.285, G.288, S.289, P.291 Ligands: ZN.13, ZN.14 12 PLIP interactions: 11 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:Y.137 Hydrogen bonds: E:G.75, E:T.106, E:R.169, E:S.289, E:S.289, D.15 Water bridges: E:D.107 Salt bridges: E:H.70, E:H.70, E:H.201, E:H.230 ASP.18: 16 residues within 4Å: Chain F: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, H.230, D.285, G.288, S.289, P.291 Ligands: ZN.16, ZN.17 17 PLIP interactions: 14 interactions with chain F, 3 Ligand-Ligand interactions Hydrophobic interactions: F:Y.137 Hydrogen bonds: F:G.75, F:T.106, F:T.106, F:Y.137, F:S.289, F:S.289, F:S.289, D.18, D.18, D.18 Water bridges: F:R.169, F:R.169 Salt bridges: F:H.70, F:H.70, F:H.201, F:H.230 ASP.21: 15 residues within 4Å: Chain G: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, D.285, G.288, S.289, P.291 Ligands: ZN.19, ZN.20 12 PLIP interactions: 11 interactions with chain G, 1 Ligand-Ligand interactions Hydrophobic interactions: G:Y.137 Hydrogen bonds: G:G.75, G:T.106, G:R.169, G:S.289, G:S.289, D.21 Water bridges: G:D.107 Salt bridges: G:H.70, G:H.70, G:H.201, G:H.230 ASP.24: 16 residues within 4Å: Chain H: H.70, G.74, G.75, E.77, G.105, T.106, Y.137, K.162, H.201, H.230, D.285, G.288, S.289, P.291 Ligands: ZN.22, ZN.23 17 PLIP interactions: 14 interactions with chain H, 3 Ligand-Ligand interactions Hydrophobic interactions: H:Y.137 Hydrogen bonds: H:G.75, H:T.106, H:T.106, H:Y.137, H:S.289, H:S.289, H:S.289, D.24, D.24, D.24 Water bridges: H:R.169, H:R.169 Salt bridges: H:H.70, H:H.70, H:H.201, H:H.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., High Resolution X-ray Structure of Isoaspartyl Dipeptidase from Escherichia coli. Biochemistry (2003)

Release Date

2003-05-06

Peptides

Isoaspartyl dipeptidase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Isoaspartyl dipeptidase

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