Research workbench
X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10Q
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
- 4ZY0
- Type
- protein
- Length
- 6,173 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
- 4TM, ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 10 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, 21% strand | A0A024V0B1 |
| B, I | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 518 | 34% 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 | 513 | 35% helix, 22% strand | A0A024V0B1 |
| E | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 509 | 35% helix, 22% strand | A0A024V0B1 |
| F | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 510 | 35% helix, 22% strand | A0A024V0B1 |
| H | 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 | 514 | 35% helix, 22% strand | A0A024V0B1 |
| K | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 508 | 35% helix, 22% strand | A0A024V0B1 |
| L | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 511 | 36% helix, 22% strand | A0A024V0B1 |
Ligands and binding sites
- 4TM · N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(thiophen-3-yl)phenyl]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 · 23 copies · chains A, B, C, E, D, F, G, H, I, K, J, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 2 copies · chains C, G
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 | 1161 | 0.78 | 0.80 | 134 | empty |
| 2 | 1155 | 0.76 | 0.79 | 125 | empty |
| 3 | 1030 | 0.74 | 0.77 | 116 | empty |
| 4 | 886 | 0.73 | 0.77 | 104 | empty |
| 5 | 872 | 0.73 | 0.78 | 71 | 4TM, CO3 |
Interfaces
26 interfaces between chains.
- H–I · 1508 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1498 Ų buried · 23 hydrogen bonds · protein-protein
- G–I · 1493 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1481 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4ZY0 · X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10q · the same entry in another collection · 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 A0A024V0B1
- Elsewhere: RCSB PDB 4ZY0 · PDBe 4ZY0 · UniProt A0A024V0B1
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