MolNFT v1 · #141210 · protein + DNA
ATVAL1 B3 domain in complex with 13BP-DNA
5YZZ · DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3'): “ATVAL1 B3 domain in complex with 13BP-DNA”. X-ray diffraction, 1 pocket (best druggability 0.47). MolNFT v1 #141210 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5YZZ
- Type
- protein + DNA
- Length
- 137 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3'); DNA…
- UniProt
- Q8W4L5
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3') | dna | 13 | — | — |
| B | DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3') | dna | 13 | — | — |
| C | B3 domain-containing transcription repressor VAL1 | protein | 111 | 15% helix, 48% strand | Q8W4L5 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.47 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 550 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- B–C · 404 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 365 Ų buried · 4 hydrogen bonds · protein-nucleic
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 Q8W4L5
- Elsewhere: RCSB PDB 5YZZ · PDBe 5YZZ · UniProt Q8W4L5
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