SMTL ID : 1onw.1

Crystal structure of Isoaspartyl Dipeptidase from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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, L.103, K.162, D.285 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.68, A:H.70, A:D.285, H2O.2 ZN.2: 6 residues within 4Å: Chain A: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.201, A:H.230, H2O.2 ZN.7: 5 residues within 4Å: Chain B: H.68, H.70, K.162, D.285 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.68, B:H.70, B:D.285, H2O.16 ZN.8: 6 residues within 4Å: Chain B: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.201, B:H.230, H2O.16 ZN.13: 6 residues within 4Å: Chain C: H.68, H.70, L.103, K.162, D.285 Ligands: ZN.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.68, C:H.70, C:D.285, H2O.31 ZN.14: 6 residues within 4Å: Chain C: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.201, C:H.230, H2O.31 ZN.19: 5 residues within 4Å: Chain D: H.68, H.70, K.162, D.285 Ligands: ZN.20 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.68, D:H.70, D:D.285, H2O.45 ZN.20: 6 residues within 4Å: Chain D: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.201, D:H.230, H2O.45 ZN.25: 6 residues within 4Å: Chain E: H.68, H.70, L.103, K.162, D.285 Ligands: ZN.26 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.68, E:H.70, E:D.285, H2O.60 ZN.26: 6 residues within 4Å: Chain E: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.25 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.201, E:H.230, H2O.60 ZN.31: 5 residues within 4Å: Chain F: H.68, H.70, K.162, D.285 Ligands: ZN.32 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.68, F:H.70, F:D.285, H2O.73 ZN.32: 6 residues within 4Å: Chain F: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.31 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.201, F:H.230, H2O.73 ZN.37: 6 residues within 4Å: Chain G: H.68, H.70, L.103, K.162, D.285 Ligands: ZN.38 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.68, G:H.70, G:D.285, H2O.88 ZN.38: 6 residues within 4Å: Chain G: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.37 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.201, G:H.230, H2O.88 ZN.43: 5 residues within 4Å: Chain H: H.68, H.70, K.162, D.285 Ligands: ZN.44 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.68, H:H.70, H:D.285, H2O.102 ZN.44: 6 residues within 4Å: Chain H: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.43 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.201, H:H.230, H2O.102

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: D.167, H.168, D.204 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: V.87, A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: D.167, H.168, D.204 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain D: V.87, A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain E: A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain E: D.167, H.168, D.204 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain F: V.87, A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.39: 5 residues within 4Å: Chain G: A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain G: D.167, H.168, D.204 Ligand excluded by PLIP CL.47: 6 residues within 4Å: Chain H: V.87, A.88, L.89, K.119, G.385, E.388 Ligand excluded by PLIP

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

EDO.5: 6 residues within 4Å: Chain A: A.153, L.191, G.192 Chain B: L.117, A.118, R.121 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.191, B:R.121 EDO.6: 6 residues within 4Å: Chain A: L.117, A.118, R.121 Chain B: A.153, L.191, G.192 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.121, B:L.191 EDO.12: 9 residues within 4Å: Chain B: W.131, I.159, G.193, K.194, P.195, N.341, L.342, T.343 Ligands: NA.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.193, B:T.343 EDO.17: 6 residues within 4Å: Chain C: A.153, L.191, G.192 Chain D: L.117, A.118, R.121 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.191, D:R.121 EDO.18: 6 residues within 4Å: Chain C: L.117, A.118, R.121 Chain D: A.153, L.191, G.192 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.121, D:L.191 EDO.24: 9 residues within 4Å: Chain D: W.131, I.159, G.193, K.194, P.195, N.341, L.342, T.343 Ligands: NA.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.193, D:T.343 EDO.29: 6 residues within 4Å: Chain E: A.153, L.191, G.192 Chain F: L.117, A.118, R.121 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:L.191, F:R.121 EDO.30: 6 residues within 4Å: Chain E: L.117, A.118, R.121 Chain F: A.153, L.191, G.192 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.121, F:L.191 EDO.36: 9 residues within 4Å: Chain F: W.131, I.159, G.193, K.194, P.195, N.341, L.342, T.343 Ligands: NA.34 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.193, F:T.343 EDO.41: 6 residues within 4Å: Chain G: A.153, L.191, G.192 Chain H: L.117, A.118, R.121 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:L.191, H:R.121 EDO.42: 6 residues within 4Å: Chain G: L.117, A.118, R.121 Chain H: A.153, L.191, G.192 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:R.121, H:L.191 EDO.48: 9 residues within 4Å: Chain H: W.131, I.159, G.193, K.194, P.195, N.341, L.342, T.343 Ligands: NA.46 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.193, H:T.343

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.10: 2 residues within 4Å: Chain B: G.193 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.193, B:G.193, B:G.193 NA.22: 2 residues within 4Å: Chain D: G.193 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.193 NA.34: 2 residues within 4Å: Chain F: G.193 Ligands: EDO.36 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.193 NA.46: 2 residues within 4Å: Chain H: G.193 Ligands: EDO.48 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.193

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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