MolNFT v1 · #161095 · protein
Structure of CHD4 PHD2 - tandem chromodomains
6Q3M · Chromodomain-helicase-DNA-binding protein 4: “Structure of CHD4 PHD2 - tandem chromodomains”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.54). MolNFT v1 #161095 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Q3M
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromodomain-helicase-DNA-binding protein 4
- EC
- 3.6.4.12
- UniProt
- Q14839
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromodomain-helicase-DNA-binding protein 4 (EC 3.6.4.12) | protein | 216 | 25% helix, 21% strand | Q14839 |
| B | Chromodomain-helicase-DNA-binding protein 4 (EC 3.6.4.12) | protein | 214 | 23% helix, 21% strand | Q14839 |
| C | Chromodomain-helicase-DNA-binding protein 4 (EC 3.6.4.12) | protein | 219 | 23% helix, 21% strand | Q14839 |
| D | Chromodomain-helicase-DNA-binding protein 4 (EC 3.6.4.12) | protein | 199 | 25% helix, 22% strand | Q14839 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.54 | 0.75 | 35 | PGE, EDO |
| 2 | 286 | 0.52 | 0.75 | 31 | PGE, EDO |
| 3 | 156 | 0.48 | 0.77 | 23 | empty |
| 4 | 221 | 0.48 | 0.74 | 27 | EDO |
| 5 | 116 | 0.47 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 735 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 334 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 330 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q14839
- Elsewhere: RCSB PDB 6Q3M · PDBe 6Q3M · UniProt Q14839
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