MolNFT v1 · #110125 · protein
Crystal structure of E. COLI aminopeptidase N in complex with L-2,3- diaminopropionic acid
4XN7: “Crystal structure of E. COLI aminopeptidase N in complex with L-2,3- diaminopropionic acid”. X-ray diffraction, 3 ligands (DPP, NA, ZN), 9 pockets (best druggability 0.84). MolNFT v1 #110125 on GenesisL1: 3D structure, binding sites…
- PDB
- 4XN7
- 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
- DPP, NA, ZN
- Pockets
- 9 · best druggability 0.84
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
- DPP · Diaminopropanoic acid · ligand · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 28 copies · 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.84 | 0.87 | 113 | DPP, NA, GOL, MLI |
| 2 | 483 | 0.73 | 0.82 | 58 | GOL |
| 3 | 603 | 0.70 | 0.78 | 57 | GOL |
| 4 | 75 | 0.60 | 0.89 | 20 | empty |
| 5 | 142 | 0.44 | 0.76 | 25 | empty |
Compared structures
- 4XN7 · Crystal Structure of E. coli Aminopeptidase N in complex with L-2,3-Diaminopropionic 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 4XN7 · PDBe 4XN7 · UniProt P04825
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