MolNFT v1 · #105092 · protein
Crystal structure of chromodomain of rhino with H3K9ME3
4QUF · RE36324P: “Crystal structure of chromodomain of rhino with H3K9ME3”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #105092 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QUF
- Type
- protein
- Length
- 400 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RE36324P; H3(1-15)K9ME3 peptide
- UniProt
- Q7JXA8
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 10 distinct chains · 34% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RE36324P | protein | 57 | 39% helix, 44% strand | Q7JXA8 |
| P, Q | H3(1-15)K9ME3 peptide | protein | 8 | 0% helix, 38% strand | — |
| B | RE36324P | protein | 63 | 44% helix, 40% strand | Q7JXA8 |
| C | RE36324P | protein | 61 | 30% helix, 41% strand | Q7JXA8 |
| R | H3(1-15)K9ME3 peptide | protein | 9 | 0% helix, 22% strand | — |
| D, E | RE36324P | protein | 58 | 38% helix, 43% strand | Q7JXA8 |
| T | H3(1-15)K9ME3 peptide | protein | 7 | 0% helix, 43% strand | — |
| V | H3(1-15)K9ME3 peptide | protein | 6 | 0% helix, 50% strand | — |
| F | RE36324P | protein | 60 | 42% helix, 40% strand | Q7JXA8 |
| U | H3(1-15)K9ME3 peptide | protein | 5 | 0% helix, 40% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.53 | 0.73 | 42 | empty |
| 2 | 124 | 0.43 | 0.76 | 14 | empty |
| 3 | 140 | 0.41 | 0.74 | 15 | empty |
Interfaces
16 interfaces between chains.
- A–B · 799 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 779 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 757 Ų buried · 14 hydrogen bonds · protein-protein
- C–R · 651 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 645 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (methylation).
Compared structures
- 4QUF · crystal structure of chromodomain of Rhino with H3K9me3 · 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 Q7JXA8
- Elsewhere: RCSB PDB 4QUF · PDBe 4QUF · UniProt Q7JXA8
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