Research workbench
Crystal structure of aminopeptidase N in complex with 2,4- diaminobutyric acid
Analyse Crystal structure of aminopeptidase N in complex with 2,4- diaminobutyric acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KED
- 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
- DAB, NA, ZN
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- DAB · 2,4-diaminobutyric acid · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- MLA · Malonic acid · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.85 | 0.87 | 113 | ZN, DAB, GOL, MLA |
| 2 | 476 | 0.73 | 0.82 | 55 | GOL |
| 3 | 602 | 0.69 | 0.78 | 60 | GOL |
| 4 | 84 | 0.60 | 0.89 | 22 | empty |
| 5 | 124 | 0.44 | 0.77 | 20 | empty |
Compared structures
- 3KED · Crystal structure of Aminopeptidase N in complex with 2,4-diaminobutyric acid · 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 3KED · PDBe 3KED · UniProt P04825
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