MolNFT v1 · #110115 · protein
Crystal structure of MET260ALA mutant of E. COLI aminopeptidase N in complex with bestatin
4XMX: “Crystal structure of MET260ALA mutant of E. COLI aminopeptidase N in complex with bestatin”. X-ray diffraction, 3 ligands (BES, NA, ZN), 8 pockets (best druggability 0.84). MolNFT v1 #110115 on GenesisL1: 3D structure, binding sites…
- PDB
- 4XMX
- 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
- BES, NA, ZN
- Pockets
- 8 · best druggability 0.84
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
- BES · 2-(3-amino-2-hydroxy-4-phenyl-butyrylamino)-4-methyl-pentanoic acid · ligand · chains A
- NA · Sodium ion · metal · 5 copies · chains A
- ZN · Zinc ion · metal · chains A
- MLI · Malonate ion · additive · 13 copies · chains A
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.84 | 0.87 | 113 | BES, MLI |
| 2 | 515 | 0.73 | 0.82 | 58 | NA, MLI |
| 3 | 576 | 0.67 | 0.77 | 60 | GOL |
| 4 | 136 | 0.43 | 0.76 | 23 | empty |
| 5 | 72 | 0.42 | 0.81 | 17 | GOL |
Compared structures
- 4XMX · Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with Bestatin · 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 4XMX · PDBe 4XMX · UniProt P04825
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