MolNFT v1 · #151396 · protein
Polyadpribosyl glycohydrolase in complex with PDD00013907
6HMM · POLY(ADP-ribose) glycohydrolase: “Polyadpribosyl glycohydrolase in complex with PDD00013907”. X-ray diffraction, 2 ligands (7JB, SO4), 4 pockets (best druggability 0.67). MolNFT v1 #151396 on GenesisL1: 3D structure, binding sites…
- PDB
- 6HMM
- Type
- protein
- Length
- 507 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
- 7JB, SO4
- Pockets
- 4 · best druggability 0.67
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 | 507 | 40% helix, 15% strand | Q86W56 |
Ligands and binding sites
- 7JB · ~{N}-~{tert}-butyl-9,10-bis(oxidanylidene)anthracene-2-sulfonamide · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · 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 | 434 | 0.67 | 0.80 | 45 | empty |
| 2 | 213 | 0.59 | 0.80 | 34 | 7JB |
| 3 | 107 | 0.44 | 0.77 | 14 | empty |
| 4 | 69 | 0.35 | 0.77 | 24 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6HMM · Polyadpribosyl glycohydrolase in complex with PDD00013907 · 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 6HMM · PDBe 6HMM · UniProt Q86W56
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