Research workbench
Crystal structure of the chaetomium thermophilum polycomb repressive complex 2 (PRC2)
Analyse Crystal structure of the chaetomium thermophilum polycomb repressive complex 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M5G
- Type
- protein
- Length
- 1,295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polycomb protein eed; Putative uncharacterized protein; Histone H3 11-mer…
- UniProt
- G0S8H7, G0SDW4
- Ligands
- SAH, ZN
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative polycomb protein eed | protein | 481 | 9% helix, 39% strand | G0S8H7 |
| B | Putative uncharacterized protein | protein | 797 | 37% helix, 13% strand | G0SDW4 |
| D | Histone H3 11-mer peptide | protein | 8 | 0% helix, 13% strand | — |
| E | Fragment from molecular 2 (region containing putative polycomb protein SUZ12) | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.86 | 0.90 | 58 | empty |
| 2 | 604 | 0.83 | 0.88 | 67 | empty |
| 3 | 543 | 0.82 | 0.88 | 81 | empty |
| 4 | 530 | 0.75 | 0.83 | 77 | empty |
| 5 | 885 | 0.74 | 0.78 | 71 | SAH |
Interfaces
4 interfaces between chains.
- A–B · 5621 Ų buried · 74 hydrogen bonds · protein-protein
- B–E · 723 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 531 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 229 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 5M5G · Crystal structure of the Chaetomium Thermophilum polycomb repressive complex 2 (PRC2) · the same entry in another collection · chain D against D, 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 G0S8H7
- Every structure of UniProt G0SDW4
- Elsewhere: RCSB PDB 5M5G · PDBe 5M5G · UniProt G0S8H7 · UniProt G0SDW4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.