MolNFT v1 · #109477 · protein
Crystal structure of chromobox homolog 7 (CBX7) chromodomain with suramin
4X3U · Chromobox protein homolog 7: “Crystal structure of chromobox homolog 7 (CBX7) chromodomain with suramin”. X-ray diffraction, 1 ligand (SVR), 2 pockets (best druggability 0.67). MolNFT v1 #109477 on GenesisL1: 3D structure, binding…
- PDB
- 4X3U
- Type
- protein
- Length
- 109 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromobox protein homolog 7
- UniProt
- Q8VDS3
- Ligands
- SVR
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromobox protein homolog 7 | protein | 56 | 30% helix, 38% strand | Q8VDS3 |
| B | Chromobox protein homolog 7 | protein | 53 | 32% helix, 42% strand | Q8VDS3 |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.67 | 0.81 | 34 | SVR |
| 2 | 90 | 0.40 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 344 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4X3U · Crystal structure of chromobox homolog 7 (CBX7) chromodomain with Suramin · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VDS3 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 7 (Q8VDS3) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 Q8VDS3
- Elsewhere: RCSB PDB 4X3U · PDBe 4X3U · UniProt Q8VDS3
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