Research workbench
PHD2 and winged-helix domain of polycomblike
Analyse PHD2 and winged-helix domain of polycomblike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OQD
- Type
- protein
- Length
- 1,121 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein pcl
- UniProt
- Q24459
- Ligands
- ZN, PO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Polycomb protein pcl | protein | 186 | 26% helix, 22% strand | Q24459 |
| A | Polycomb protein pcl | protein | 184 | 27% helix, 18% strand | Q24459 |
| C | Polycomb protein pcl | protein | 192 | 29% helix, 14% strand | Q24459 |
| D | Polycomb protein pcl | protein | 187 | 28% helix, 16% strand | Q24459 |
| E | Polycomb protein pcl | protein | 180 | 26% helix, 15% strand | Q24459 |
| F | Polycomb protein pcl | protein | 192 | 26% helix, 14% strand | Q24459 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains B, A, C, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains C, B, A, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.81 | 0.84 | 110 | EDO |
| 2 | 859 | 0.77 | 0.80 | 61 | empty |
| 3 | 710 | 0.75 | 0.81 | 68 | empty |
| 4 | 108 | 0.62 | 0.87 | 19 | empty |
| 5 | 87 | 0.61 | 0.88 | 21 | empty |
Interfaces
10 interfaces between chains.
- B–A · 1523 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 448 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 256 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 200 Ų buried · 2 hydrogen bonds · protein-protein
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 Q24459
- Elsewhere: RCSB PDB 5OQD · PDBe 5OQD · UniProt Q24459
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