MolNFT v1 · #147470 · protein
X-ray crystal structure of pf-M1 in complex with inhibitor (6K) and catalytic zinc ion
6EE3 · M1 family aminopeptidase: “X-ray crystal structure of pf-M1 in complex with inhibitor (6K) and catalytic zinc ion”. X-ray diffraction, 4 ligands (J4V, MG, ZN), 12 pockets (best druggability 0.83). MolNFT v1 #147470 on GenesisL1: 3D…
- PDB
- 6EE3
- Type
- protein
- Length
- 889 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1 family aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O96935
- Ligands
- J4V, MG, ZN, PO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 889 | 45% helix, 21% strand | O96935 |
Ligands and binding sites
- J4V · (1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.83 | 0.87 | 96 | ZN, J4V |
| 2 | 220 | 0.69 | 0.86 | 29 | empty |
| 3 | 80 | 0.64 | 0.91 | 23 | empty |
| 4 | 59 | 0.58 | 0.90 | 18 | empty |
| 5 | 81 | 0.55 | 0.86 | 20 | empty |
Compared structures
- 6EE3 · X-ray crystal structure of Pf-M1 in complex with inhibitor (6k) and catalytic zinc ion · the same entry in another collection · chain A against A, TM-score 1.00
- O96935 · AlphaFold monomer V2.0 prediction for M1 family aminopeptidase (O96935) · 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 O96935
- Elsewhere: RCSB PDB 6EE3 · PDBe 6EE3 · UniProt O96935
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