Research workbench
X-ray crystal structure of pfa-M1 in complex with hydroxamic acid- based inhibitor 9Q
Analyse X-ray crystal structure of pfa-M1 in complex with hydroxamic acid- based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZW6
- 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
- 4SY, MG, ZN, PO4
- Pockets
- 13 · 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
- 4SY · tert-butyl {(1S)-2-(hydroxyamino)-1-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-2-oxoethyl}carbamate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.80 | 0.87 | 59 | 4SY, ZN, GOL, DMS |
| 2 | 225 | 0.70 | 0.86 | 35 | GOL |
| 3 | 657 | 0.69 | 0.77 | 62 | PO4 |
| 4 | 143 | 0.63 | 0.86 | 27 | DMS |
| 5 | 67 | 0.62 | 0.91 | 19 | empty |
Compared structures
- 4ZW6 · X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 9q · 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 4ZW6 · PDBe 4ZW6 · UniProt O96935
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