MolNFT v1 · #115167 · protein
Crystal structure of pfa-M17 with virtual ligand inhibitor
5CBM · M17 family aminopeptidase: “Crystal structure of pfa-M17 with virtual ligand inhibitor”. X-ray diffraction, 4 ligands (4ZN, ZN, SO4), 20 pockets (best druggability 0.74). MolNFT v1 #115167 on GenesisL1: 3D structure, binding sites…
- PDB
- 5CBM
- Type
- protein
- Length
- 6,173 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M17 family aminopeptidase
- UniProt
- A0A024V0B1
- Ligands
- 4ZN, ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | M17 family aminopeptidase | protein | 519 | 35% helix, 21% strand | A0A024V0B1 |
| B | M17 family aminopeptidase | protein | 516 | 34% helix, 22% strand | A0A024V0B1 |
| C, I | M17 family aminopeptidase | protein | 517 | 35% helix, 22% strand | A0A024V0B1 |
| D, J | M17 family aminopeptidase | protein | 514 | 36% helix, 22% strand | A0A024V0B1 |
| E, K | M17 family aminopeptidase | protein | 509 | 35% helix, 22% strand | A0A024V0B1 |
| F, L | M17 family aminopeptidase | protein | 511 | 35% helix, 21% strand | A0A024V0B1 |
| H | M17 family aminopeptidase | protein | 517 | 35% helix, 22% strand | A0A024V0B1 |
Ligands and binding sites
- 4ZN · (2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid · 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, F, B, C, E, 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 · 25 copies · chains A, B, C, D, E, F, G, H, I, J, L, K
- GOL · Glycerol · 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 | 1062 | 0.74 | 0.77 | 119 | empty |
| 2 | 839 | 0.74 | 0.78 | 59 | SO4 |
| 3 | 704 | 0.73 | 0.79 | 69 | CO3, 4ZN |
| 4 | 722 | 0.72 | 0.79 | 74 | CO3, 4ZN, SO4 |
| 5 | 882 | 0.72 | 0.77 | 95 | SO4 |
Interfaces
26 interfaces between chains.
- B–C · 1513 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1509 Ų buried · 24 hydrogen bonds · protein-protein
- G–I · 1500 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1494 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1463 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5CBM · Crystal structure of PfA-M17 with virtual ligand inhibitor · 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 5CBM · PDBe 5CBM · UniProt A0A024V0B1
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