MolNFT v1 · #123345 · protein
Structural basis for the hierarchical assembly of the core of PRC1.1
5JH5 · Lysine-specific demethylase 2B: “Structural basis for the hierarchical assembly of the core of PRC1.1”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #123345 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5JH5
- Type
- protein
- Length
- 609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 2B; S-phase kinase-associated protein 1; Polycomb group ring…
- EC
- 1.14.11.27
- UniProt
- Q8NHM5, P63208, Q9BSM1, Q5H9F3
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 2B (EC 1.14.11.27) | protein | 267 | 37% helix, 13% strand | Q8NHM5 |
| B | S-phase kinase-associated protein 1 | protein | 149 | 52% helix, 8% strand | P63208 |
| C | Polycomb group ring finger protein 1 | protein | 88 | 30% helix, 34% strand | Q9BSM1 |
| D | BCL-6 corepressor-like protein 1 | protein | 105 | 29% helix, 30% strand | Q5H9F3 |
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 | 306 | 0.68 | 0.83 | 51 | empty |
| 2 | 148 | 0.60 | 0.84 | 24 | empty |
| 3 | 236 | 0.48 | 0.74 | 28 | empty |
| 4 | 97 | 0.45 | 0.80 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1531 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1371 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 839 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 367 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 5JH5 · Structural Basis for the Hierarchical Assembly of the Core of PRC1.1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BSM1 · AlphaFold monomer V2.0 prediction for polycomb group ring finger protein 1 (Q9BSM1) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q8NHM5 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 2B (Q8NHM5) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q5H9F3 · AlphaFold monomer V2.0 prediction for BCL-6 corepressor-like protein 1 (Q5H9F3) · a predicted model of the same protein · chain D against A, TM-score 0.90
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 Q8NHM5
- Every structure of UniProt P63208
- Every structure of UniProt Q9BSM1
- Every structure of UniProt Q5H9F3
- Elsewhere: RCSB PDB 5JH5 · PDBe 5JH5 · UniProt Q8NHM5 · UniProt P63208 · UniProt Q9BSM1 · UniProt Q5H9F3
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