MolNFT v1 · #137295 · protein
Apo CTPRC2 with E840A and K852D mutations in EZH2
5VK3 · Polycomb protein eed: “Apo CTPRC2 with E840A and K852D mutations in EZH2”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #137295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VK3
- Type
- protein
- Length
- 1,262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed; Histone-lysine N-methyltransferase EZH2,POLYCOMB protein SUZ12
- UniProt
- G0S8H7, G0SDW4, G0RYC6
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 468 | 9% helix, 40% strand | G0S8H7 |
| B | Histone-lysine N-methyltransferase EZH2,POLYCOMB protein SUZ12 | protein | 794 | 37% helix, 12% strand | G0SDW4, G0RYC6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.86 | 0.88 | 76 | empty |
| 2 | 606 | 0.84 | 0.89 | 93 | empty |
| 3 | 527 | 0.84 | 0.90 | 67 | empty |
| 4 | 320 | 0.73 | 0.85 | 47 | empty |
| 5 | 482 | 0.72 | 0.82 | 64 | empty |
Interfaces
1 interface between chains.
- A–B · 5302 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 5VK3 · Apo ctPRC2 with E840A and K852D mutations in Ezh2 · the same entry in another collection · 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 G0S8H7
- Every structure of UniProt G0SDW4
- Every structure of UniProt G0RYC6
- Elsewhere: RCSB PDB 5VK3 · PDBe 5VK3 · UniProt G0S8H7 · UniProt G0SDW4 · UniProt G0RYC6
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