Research workbench
Crystal structure of E. COLI aminopeptidase N in complex with beta alanine
Analyse Crystal structure of E. COLI aminopeptidase N in complex with beta alanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XN9
- Type
- protein
- Length
- 866 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P04825
- Ligands
- BAL, NA, ZN
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 866 | 45% helix, 22% strand | P04825 |
Ligands and binding sites
- BAL · Beta-alanine · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- MLI · Malonate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.85 | 0.87 | 110 | BAL |
| 2 | 481 | 0.72 | 0.81 | 61 | MLI |
| 3 | 657 | 0.72 | 0.79 | 58 | empty |
| 4 | 51 | 0.55 | 0.90 | 20 | empty |
| 5 | 69 | 0.44 | 0.82 | 18 | empty |
Compared structures
- 4XN9 · Crystal Structure of E. coli Aminopeptidase N in complex with Beta Alanine · the same entry in another collection · chain A against A, TM-score 1.00
- P04825 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P04825) · a predicted model of the same protein · 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 P04825
- Elsewhere: RCSB PDB 4XN9 · PDBe 4XN9 · UniProt P04825
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