Research workbench
X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 9B
Analyse X-ray crystal structure of pfa-M17 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
- 4ZX8
- Type
- protein
- Length
- 6,174 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable M17 family aminopeptidase
- EC
- 3.4.11.1
- UniProt
- A0A024V0B1
- Ligands
- 4TY, ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 11 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 519 | 35% helix, 22% strand | A0A024V0B1 |
| B | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 516 | 35% helix, 22% strand | A0A024V0B1 |
| C | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 517 | 35% helix, 22% strand | A0A024V0B1 |
| D | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 512 | 36% helix, 22% strand | A0A024V0B1 |
| E | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 510 | 35% helix, 22% strand | A0A024V0B1 |
| F | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 513 | 36% helix, 22% strand | A0A024V0B1 |
| H | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 517 | 35% helix, 22% strand | A0A024V0B1 |
| I | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 517 | 35% helix, 22% strand | A0A024V0B1 |
| J | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 513 | 35% helix, 22% strand | A0A024V0B1 |
| K | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 509 | 35% helix, 22% strand | A0A024V0B1 |
| L | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 512 | 35% helix, 22% strand | A0A024V0B1 |
Ligands and binding sites
- 4TY · Tert-butyl [(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]carbamate · 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 · 13 copies · chains A, B, C, D, E, F, G, H, I, J, 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 · 26 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 6 copies · chains A, D, F, C, E, I, J
- DMS · Dimethyl sulfoxide · additive · chains A
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 | 757 | 0.73 | 0.78 | 56 | empty |
| 2 | 704 | 0.72 | 0.79 | 81 | empty |
| 3 | 821 | 0.72 | 0.77 | 70 | 4TY, CO3 |
| 4 | 806 | 0.72 | 0.77 | 90 | empty |
| 5 | 750 | 0.72 | 0.78 | 71 | 4TY, CO3 |
Interfaces
26 interfaces between chains.
- A–C · 1496 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1494 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1494 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1492 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1489 Ų buried · 24 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 A0A024V0B1
- Elsewhere: RCSB PDB 4ZX8 · PDBe 4ZX8 · UniProt A0A024V0B1
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