Research workbench
Zn-dependent D-aminopeptidase dppa from bacillus subtilis, a self- compartmentalizing protease.
Analyse Zn-dependent D-aminopeptidase dppa from bacillus subtilis, a self… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HI9
- Type
- protein
- Length
- 1,370 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptide transport protein dppa
- UniProt
- P26902
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Dipeptide transport protein dppa | protein | 274 | 32% helix, 25% strand | P26902 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.63 | 0.78 | 37 | ZN |
| 2 | 359 | 0.62 | 0.78 | 35 | empty |
| 3 | 374 | 0.61 | 0.77 | 33 | ZN |
| 4 | 383 | 0.61 | 0.77 | 35 | ZN |
| 5 | 345 | 0.61 | 0.78 | 37 | ZN |
Interfaces
5 interfaces between chains.
- D–E · 897 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 894 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 889 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 886 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 876 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1HI9 · Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing… · the same entry in another collection · chain E against E, TM-score 1.00
- P26902 · AlphaFold monomer V2.0 prediction for D-aminopeptidase (P26902) · a predicted model of the same protein · chain E against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P26902
- Elsewhere: RCSB PDB 1HI9 · PDBe 1HI9 · UniProt P26902
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