Research workbench
X-ray crystal structure of pf-M1 in complex with inhibitor (6M) and catalytic zinc ion
Analyse X-ray crystal structure of pf-M1 in complex with inhibitor (6M) and catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EE4
- 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
- J4S, MG, ZN, PO4
- Pockets
- 12 · best druggability 0.80
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
- J4S · (2R)-2-[(cyclopropylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 5 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 | 533 | 0.80 | 0.87 | 70 | J4S, GOL, PO4, MG |
| 2 | 435 | 0.77 | 0.86 | 63 | empty |
| 3 | 80 | 0.68 | 0.93 | 21 | empty |
| 4 | 84 | 0.56 | 0.87 | 20 | empty |
| 5 | 51 | 0.55 | 0.90 | 15 | GOL |
Compared structures
- 6EE4 · X-ray crystal structure of Pf-M1 in complex with inhibitor (6m) 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 6EE4 · PDBe 6EE4 · UniProt O96935
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