MolNFT v1 · #112857 · protein
X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10O
4ZY2 · Probable M17 family aminopeptidase: “X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10O”. X-ray diffraction, 4 ligands (4TL, ZN, SO4), 20 pockets (best druggability 0.77). MolNFT v1 #112857 on…
- PDB
- 4ZY2
- Type
- protein
- Length
- 6,185 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable M17 family aminopeptidase
- UniProt
- A0A0L7M119
- Ligands
- 4TL, ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 10 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable M17 family aminopeptidase | protein | 519 | 35% helix, 22% strand | A0A0L7M119 |
| B | Probable M17 family aminopeptidase | protein | 517 | 36% helix, 22% strand | A0A0L7M119 |
| C, H, I | Probable M17 family aminopeptidase | protein | 518 | 35% helix, 22% strand | A0A0L7M119 |
| D | Probable M17 family aminopeptidase | protein | 513 | 36% helix, 22% strand | A0A0L7M119 |
| E | Probable M17 family aminopeptidase | protein | 513 | 35% helix, 22% strand | A0A0L7M119 |
| F | Probable M17 family aminopeptidase | protein | 512 | 35% helix, 22% strand | A0A0L7M119 |
| G | Probable M17 family aminopeptidase | protein | 518 | 35% helix, 22% strand | A0A0L7M119 |
| J | Probable M17 family aminopeptidase | protein | 514 | 35% helix, 22% strand | A0A0L7M119 |
| K | Probable M17 family aminopeptidase | protein | 512 | 36% helix, 21% strand | A0A0L7M119 |
| L | Probable M17 family aminopeptidase | protein | 513 | 36% helix, 21% strand | A0A0L7M119 |
Ligands and binding sites
- 4TL · N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 28 copies · chains A, D, B, C, E, F, G, J, I, H, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 39 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, D, G, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.77 | 0.82 | 97 | SO4, 1PE |
| 2 | 949 | 0.76 | 0.79 | 74 | SO4 |
| 3 | 1030 | 0.75 | 0.78 | 103 | DMS |
| 4 | 859 | 0.73 | 0.78 | 70 | CO3, 4TL |
| 5 | 900 | 0.73 | 0.77 | 71 | CO3, 4TL |
Interfaces
26 interfaces between chains.
- J–K · 1544 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1521 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1511 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1505 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1497 Ų buried · 23 hydrogen bonds · protein-protein
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 A0A0L7M119
- Elsewhere: RCSB PDB 4ZY2 · PDBe 4ZY2 · UniProt A0A0L7M119
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