MolNFT v2 · #221128 · protein + DNA
CDCA7 (Mouse) Binds Non-B-form 34-mer DNA oligo
8TLG · Cell division cycle-associated protein 7: “CDCA7 (Mouse) Binds Non-B-form 34-mer DNA oligo”. X-ray diffraction at 2.09, 2 ligands (ZN, MG), 3 pockets (best druggability 0.48). MolNFT v2 #221128 on GenesisL1: 3D structure, binding…
- PDB
- 8TLG
- Type
- protein + DNA
- Length
- 137 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- Cell division cycle-associated protein 7; DNA (34-mer)
- UniProt
- Q9D0M2
- Ligands
- ZN, MG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · resolution 2.09 · 2 distinct chains · 27% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division cycle-associated protein 7 | protein | 103 | 27% helix, 7% strand | Q9D0M2 |
| X | DNA (34-mer) | dna | 34 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · chains A, X
- EDO · 1,2-ethanediol · additive · 2 copies · chains X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.48 | 0.77 | 29 | empty |
| 2 | 195 | 0.47 | 0.75 | 19 | empty |
| 3 | 105 | 0.45 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–X · 740 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- Q9D0M2 · AlphaFold monomer V2.0 prediction for cell division cycle-associated protein 7 (Q9D0M2) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9D0M2
- Elsewhere: RCSB PDB 8TLG · PDBe 8TLG · UniProt Q9D0M2
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