Research workbench
Crystal structure of E.COLI aminopeptidase N in complex with amastatin
Analyse Crystal structure of E.COLI aminopeptidase N in complex with amastatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q4I
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N; Amastatin
- EC
- 3.4.11.2
- UniProt
- P04825
- Ligands
- L2O, NA, ZN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 866 | 44% helix, 22% strand | P04825 |
| C | Amastatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- L2O · (2S,3R)-3-amino-2-hydroxy-5-methylhexanoic acid · ligand · chains A, C
- NA · Sodium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.80 | 0.87 | 72 | empty |
| 2 | 326 | 0.74 | 0.86 | 50 | empty |
| 3 | 317 | 0.74 | 0.86 | 37 | GOL |
| 4 | 66 | 0.72 | 0.98 | 24 | L2O |
| 5 | 560 | 0.67 | 0.77 | 56 | empty |
Interfaces
1 interface between chains.
- A–C · 342 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 P04825
- Elsewhere: RCSB PDB 4Q4I · PDBe 4Q4I · UniProt P04825
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.