Research workbench
The CHD1 DNA-binding domain in complex with 17MER DNA duplex
Analyse The CHD1 DNA-binding domain in complex with 17MER DNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J70
- Type
- protein + DNA
- Length
- 525 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromo domain-containing protein 1; DNA (5'- D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*…
- EC
- 3.6.4.-
- UniProt
- P32657
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 229 | 60% helix, 4% strand | P32657 |
| B | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 228 | 58% helix, 4% strand | P32657 |
| W, Y | DNA (5'- D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3') | dna | 17 | — | — |
| X, Z | DNA (5'- D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3') | dna | 17 | — | — |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.75 | 0.79 | 55 | empty |
| 2 | 1171 | 0.73 | 0.77 | 62 | empty |
| 3 | 398 | 0.62 | 0.77 | 45 | empty |
| 4 | 206 | 0.59 | 0.81 | 23 | empty |
| 5 | 120 | 0.37 | 0.74 | 17 | empty |
Interfaces
7 interfaces between chains.
- W–X · 769 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- Y–Z · 754 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–X · 460 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–Z · 431 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 396 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5J70 · The Chd1 DNA-binding domain in complex with 17mer DNA duplex · the same entry in another collection · chain Z against Z, TM-score 1.00
- P32657 · AlphaFold monomer V2.0 prediction for chromo domain-containing protein 1 (P32657) · a predicted model of the same protein · chain A 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 P32657
- Elsewhere: RCSB PDB 5J70 · PDBe 5J70 · UniProt P32657
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