MolNFT v1 · #112881 · protein
X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10S
4ZYQ · Probable M17 family aminopeptidase: “X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10S”. X-ray diffraction, 4 ligands (4U6, ZN, CO3), 20 pockets (best druggability 0.76). MolNFT v1 #112881 on…
- PDB
- 4ZYQ
- Type
- protein
- Length
- 6,168 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
- 4U6, ZN, CO3, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 10 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 517 | 35% helix, 22% strand | A0A024V0B1 |
| B, H | 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 | 516 | 35% helix, 22% strand | A0A024V0B1 |
| D | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 514 | 35% helix, 22% strand | A0A024V0B1 |
| E | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 509 | 35% helix, 22% strand | A0A024V0B1 |
| F, L | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 511 | 35% helix, 22% strand | A0A024V0B1 |
| G | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 519 | 35% helix, 22% strand | A0A024V0B1 |
| I | Probable M17 family aminopeptidase (EC 3.4.11.1) | protein | 518 | 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 | 508 | 35% helix, 22% strand | A0A024V0B1 |
Ligands and binding sites
- 4U6 · N-{(1R)-2-(hydroxyamino)-1-[3'-(N'-hydroxycarbamimidoyl)biphenyl-4-yl]-2-oxoethyl}-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
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, 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 | 844 | 0.76 | 0.80 | 78 | empty |
| 2 | 942 | 0.75 | 0.78 | 92 | empty |
| 3 | 836 | 0.74 | 0.78 | 78 | 4U6 |
| 4 | 902 | 0.73 | 0.77 | 69 | 4U6, CO3 |
| 5 | 861 | 0.73 | 0.78 | 98 | empty |
Interfaces
26 interfaces between chains.
- B–C · 1489 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1486 Ų buried · 22 hydrogen bonds · protein-protein
- G–I · 1482 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1479 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1476 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4ZYQ · X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10s · the same entry in another collection · chain D against D, 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 4ZYQ · PDBe 4ZYQ · UniProt A0A024V0B1
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