MolNFT v1 · #126869 · protein
The crystal structure of E. COLI aminopeptidase N in complex with 7- amino-1-bromo-4-phenyl-5,7,8,9-tetrahydrobenzocyclohepten-6-one
5MFT: “The crystal structure of E. COLI aminopeptidase N in complex with 7…”. X-ray diffraction, 4 ligands (7MF, NA, ZN), 10 pockets (best druggability 0.83). MolNFT v1 #126869 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFT
- Type
- protein
- Length
- 868 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
- 7MF, NA, ZN, CL
- Pockets
- 10 · best druggability 0.83
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 | 868 | 44% helix, 22% strand | P04825 |
Ligands and binding sites
- 7MF · [(7~{S})-1-bromanyl-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium · ligand · chains A
- NA · Sodium ion · metal · 6 copies · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 8 copies · chains A
- MLI · Malonate ion · additive · 5 copies · chains A
- DMS · Dimethyl sulfoxide · 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 | 677 | 0.83 | 0.88 | 92 | GOL |
| 2 | 330 | 0.72 | 0.84 | 36 | MLI |
| 3 | 674 | 0.70 | 0.78 | 65 | NA, MLI |
| 4 | 192 | 0.69 | 0.87 | 33 | 7MF |
| 5 | 136 | 0.48 | 0.79 | 31 | DMS |
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 5MFT · PDBe 5MFT · UniProt P04825
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