MolNFT v1 · #151394 · protein
Polyadpribosyl glycohydrolase in complex with PDD00016690
6HMK · POLY(ADP-ribose) glycohydrolase: “Polyadpribosyl glycohydrolase in complex with PDD00016690”. X-ray diffraction, 2 ligands (7JC, SO4), 4 pockets (best druggability 0.69). MolNFT v1 #151394 on GenesisL1: 3D structure, binding sites…
- PDB
- 6HMK
- Type
- protein
- Length
- 506 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
- 7JC, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 506 | 40% helix, 15% strand | Q86W56 |
Ligands and binding sites
- 7JC · 1-methyl-~{N}-(1-methylcyclopropyl)-3-[(2-methyl-1,3-thiazol-5-yl)methyl]-2,4-bis(oxidanylidene) quinazoline-6-sulfonamide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
- GOL · Glycerol · additive · 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 | 493 | 0.69 | 0.79 | 46 | empty |
| 2 | 188 | 0.58 | 0.81 | 34 | 7JC |
| 3 | 53 | 0.33 | 0.78 | 20 | empty |
| 4 | 57 | 0.29 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6HMK · Polyadpribosyl glycohydrolase in complex with PDD00016690 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86W56 · AlphaFold monomer V2.0 prediction for POLY(ADP-ribose) glycohydrolase (Q86W56) · a predicted model of the same protein · 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 Q86W56
- Elsewhere: RCSB PDB 6HMK · PDBe 6HMK · UniProt Q86W56
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