MolNFT v1 · #32714 · protein
Histone fold heterodimer of the chromatin accessibility complex
2BYM · Chrac-16: “Histone fold heterodimer of the chromatin accessibility complex”. X-ray diffraction, 1 ligand (CD), 2 pockets (best druggability 0.69). MolNFT v1 #32714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BYM
- Type
- protein
- Length
- 298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chrac-16; Chrac-14
- UniProt
- Q9V452, Q9V444
- Ligands
- CD
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chrac-16 | protein | 65 | 62% helix, 3% strand | Q9V452 |
| B | Chrac-14 | protein | 83 | 71% helix, 2% strand | Q9V444 |
| C | Chrac-16 | protein | 64 | 67% helix, 3% strand | Q9V452 |
| D | Chrac-14 | protein | 86 | 72% helix, 2% strand | Q9V444 |
Ligands and binding sites
- CD · Cadmium ion · metal · 3 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.69 | 0.78 | 34 | empty |
| 2 | 148 | 0.50 | 0.79 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1792 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1778 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 358 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 281 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2BYM · Histone fold heterodimer of the Chromatin Accessibility Complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9V444 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon subunit 3 (Q9V444) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9V452 · AlphaFold monomer V2.0 prediction for chromatin accessibility complex 16KD protein… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q9V452
- Every structure of UniProt Q9V444
- Elsewhere: RCSB PDB 2BYM · PDBe 2BYM · UniProt Q9V452 · UniProt Q9V444
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