SMTL ID : 1ybq.1

Crystal structure of Escherichia coli isoaspartyl dipeptidase mutant D285N complexed with beta-aspartylhistidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.68, H.70, N.285 Ligands: ZN.2, BDH.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.68, A:H.70, H2O.5 ZN.2: 6 residues within 4Å: Chain A: Y.137, K.162, H.201, H.230 Ligands: ZN.1, BDH.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.201, A:H.230, H2O.5 ZN.4: 7 residues within 4Å: Chain B: H.68, H.70, L.103, K.162, N.285 Ligands: ZN.5, BDH.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.68, B:H.70 ZN.5: 7 residues within 4Å: Chain B: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.4, BDH.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.201, B:H.230 ZN.7: 5 residues within 4Å: Chain C: H.68, H.70, N.285 Ligands: ZN.8, BDH.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.68, C:H.70, H2O.14 ZN.8: 6 residues within 4Å: Chain C: Y.137, K.162, H.201, H.230 Ligands: ZN.7, BDH.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.201, C:H.230, H2O.14 ZN.10: 7 residues within 4Å: Chain D: H.68, H.70, L.103, K.162, N.285 Ligands: ZN.11, BDH.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.68, D:H.70 ZN.11: 7 residues within 4Å: Chain D: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.10, BDH.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.201, D:H.230 ZN.13: 5 residues within 4Å: Chain E: H.68, H.70, N.285 Ligands: ZN.14, BDH.15 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.68, E:H.70, H2O.23 ZN.14: 6 residues within 4Å: Chain E: Y.137, K.162, H.201, H.230 Ligands: ZN.13, BDH.15 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.201, E:H.230, H2O.23 ZN.16: 7 residues within 4Å: Chain F: H.68, H.70, L.103, K.162, N.285 Ligands: ZN.17, BDH.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.68, F:H.70 ZN.17: 7 residues within 4Å: Chain F: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.16, BDH.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.201, F:H.230 ZN.19: 5 residues within 4Å: Chain G: H.68, H.70, N.285 Ligands: ZN.20, BDH.21 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.68, G:H.70, H2O.33 ZN.20: 6 residues within 4Å: Chain G: Y.137, K.162, H.201, H.230 Ligands: ZN.19, BDH.21 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.201, G:H.230, H2O.33 ZN.22: 7 residues within 4Å: Chain H: H.68, H.70, L.103, K.162, N.285 Ligands: ZN.23, BDH.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.68, H:H.70 ZN.23: 7 residues within 4Å: Chain H: H.68, Y.137, K.162, H.201, H.230 Ligands: ZN.22, BDH.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.201, H:H.230

8 x BDH: L-BETA-ASPARTYLHISTIDINE(Non-covalent)

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

Links

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Citation

Marti-Arbona, R. et al., Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli. Biochemistry (2005)

Release Date

2005-04-26

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