MolNFT v1 · #151397 · protein
Polyadpribosyl glycosidase in complex with PDD00014909
6HMN · POLY(ADP-ribose) glycohydrolase: “Polyadpribosyl glycosidase in complex with PDD00014909”. X-ray diffraction, 2 ligands (70J, SO4), 6 pockets (best druggability 0.66). MolNFT v1 #151397 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HMN
- Type
- protein
- Length
- 505 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(ADP-ribose) glycohydrolase
- EC
- 3.2.1.143
- UniProt
- Q86W56
- Ligands
- 70J, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 505 | 39% helix, 15% strand | Q86W56 |
Ligands and binding sites
- 70J · 3-methyl-6-[[(1-methylcyclopropyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-1-(phenylmethyl)quinazoline-2,4-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.66 | 0.78 | 42 | empty |
| 2 | 166 | 0.56 | 0.81 | 27 | 70J |
| 3 | 98 | 0.41 | 0.77 | 14 | empty |
| 4 | 71 | 0.38 | 0.79 | 22 | empty |
| 5 | 61 | 0.33 | 0.77 | 14 | empty |
Compared structures
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 Q86W56
- Elsewhere: RCSB PDB 6HMN · PDBe 6HMN · UniProt Q86W56
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