Research workbench
Structure of a putative aminopeptidase P from bacillus anthracis
Analyse Structure of a putative aminopeptidase P from bacillus anthracis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IG4
- Type
- protein
- Length
- 2,514 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro aminopeptidase
- UniProt
- Q81RY4
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Xaa-pro aminopeptidase | protein | 419 | 39% helix, 21% strand | Q81RY4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 38 copies · chains A, B, C, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.86 | 0.87 | 113 | MN, SO4 |
| 2 | 1073 | 0.86 | 0.87 | 107 | MN, SO4 |
| 3 | 1112 | 0.85 | 0.86 | 111 | MN, SO4 |
| 4 | 689 | 0.84 | 0.88 | 83 | empty |
| 5 | 781 | 0.84 | 0.87 | 76 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2197 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2153 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2140 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 871 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 859 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 3IG4 · Structure of a putative aminopeptidase P from Bacillus anthracis · the same entry in another collection · chain A 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 Q81RY4
- Elsewhere: RCSB PDB 3IG4 · PDBe 3IG4 · UniProt Q81RY4
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