SMTL ID : 1hi9.1

Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing protease.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-10-mer

Ligands

20 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:H.104, A:E.133, A:E.133, H2O.3 ZN.2: 4 residues within 4Å: Chain A: D.8, E.10, H.60 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:E.10, A:E.10, A:H.60, H2O.3 ZN.3: 6 residues within 4Å: Chain B: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:H.104, B:E.133, B:E.133, H2O.4 ZN.4: 4 residues within 4Å: Chain B: D.8, E.10, H.60 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:E.10, B:E.10, B:H.60, H2O.4 ZN.5: 6 residues within 4Å: Chain C: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.8, C:H.104, C:E.133, C:E.133, H2O.5 ZN.6: 4 residues within 4Å: Chain C: D.8, E.10, H.60 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.8, C:E.10, C:E.10, C:H.60, H2O.5 ZN.7: 6 residues within 4Å: Chain D: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.8, D:H.104, D:E.133, D:E.133, H2O.7 ZN.8: 4 residues within 4Å: Chain D: D.8, E.10, H.60 Ligands: ZN.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.8, D:E.10, D:E.10, D:H.60, H2O.7 ZN.9: 6 residues within 4Å: Chain E: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.8, E:H.104, E:E.133, E:E.133, H2O.10 ZN.10: 4 residues within 4Å: Chain E: D.8, E.10, H.60 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.8, E:E.10, E:E.10, E:H.60, H2O.10 ZN.11: 6 residues within 4Å: Chain F: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.12 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.8, F:H.104, F:E.133, F:E.133, H2O.12 ZN.12: 4 residues within 4Å: Chain F: D.8, E.10, H.60 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.8, F:E.10, F:E.10, F:H.60, H2O.12 ZN.13: 6 residues within 4Å: Chain G: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.14 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.8, G:H.104, G:E.133, G:E.133, H2O.13 ZN.14: 4 residues within 4Å: Chain G: D.8, E.10, H.60 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.8, G:E.10, G:E.10, G:H.60, H2O.13 ZN.15: 6 residues within 4Å: Chain H: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.16 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.8, H:H.104, H:E.133, H:E.133, H2O.15 ZN.16: 4 residues within 4Å: Chain H: D.8, E.10, H.60 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.8, H:E.10, H:E.10, H:H.60, H2O.15 ZN.17: 6 residues within 4Å: Chain I: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.8, I:H.104, I:E.133, I:E.133, H2O.17 ZN.18: 4 residues within 4Å: Chain I: D.8, E.10, H.60 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.8, I:E.10, I:E.10, I:H.60, H2O.17 ZN.19: 6 residues within 4Å: Chain J: D.8, E.10, H.104, H.115, E.133 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.8, J:H.104, J:E.133, J:E.133, H2O.19 ZN.20: 4 residues within 4Å: Chain J: D.8, E.10, H.60 Ligands: ZN.19 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.8, J:E.10, J:E.10, J:H.60, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Remaut, H. et al., Structure of the Bacillus Subtilis D-Aminopeptidase Dppa Reveals a Novel Self-Compartmentalizing Protease. Nat.Struct.Biol. (2001)

Release Date

2001-08-09

Peptides

DIPEPTIDE TRANSPORT PROTEIN DPPA: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

DIPEPTIDE TRANSPORT PROTEIN DPPA