MolNFT v1 · #151395 · protein
Polyadpribosyl glycosidase in complex with PDD00017299
6HML · POLY(ADP-ribose) glycohydrolase: “Polyadpribosyl glycosidase in complex with PDD00017299”. X-ray diffraction, 2 ligands (73L, SO4), 4 pockets (best druggability 0.61). MolNFT v1 #151395 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HML
- Type
- protein
- Length
- 501 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
- 73L, SO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 501 | 41% helix, 15% strand | Q86W56 |
Ligands and binding sites
- 73L · 1-[(2,4-dimethyl-1,3-thiazol-5-yl)methyl]-6-[[(1-methylcyclopropyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-3-[(1-methylpyrazol-4-yl)methyl]quinazoline-2,4-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.61 | 0.76 | 35 | empty |
| 2 | 196 | 0.58 | 0.80 | 33 | 73L |
| 3 | 57 | 0.36 | 0.79 | 22 | GOL |
| 4 | 84 | 0.35 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
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 6HML · PDBe 6HML · UniProt Q86W56
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