MolNFT v1 · #168722 · protein + DNA
Structure of AVAR1 bound to DNA half-site
6WPA: “Structure of AVAR1 bound to DNA half-site”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #168722 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WPA
- Type
- protein + DNA
- Length
- 1,752 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AVAR1; PAL2-1-5'-gc
- UniProt
- Q82H41
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AVAR1 | protein | 215 | 73% helix, 1% strand | Q82H41 |
| B | AVAR1 | protein | 214 | 71% helix, 1% strand | Q82H41 |
| M, N | PAL2-1-5'-gc | dna | 28 | — | — |
| C, E | AVAR1 | protein | 212 | 68% helix, 1% strand | Q82H41 |
| D | AVAR1 | protein | 213 | 69% helix, 1% strand | Q82H41 |
| F, G, H | AVAR1 | protein | 210 | 69% helix, 1% strand | Q82H41 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.77 | 0.97 | 27 | empty |
| 2 | 731 | 0.76 | 0.81 | 67 | empty |
| 3 | 65 | 0.74 | 0.99 | 16 | empty |
| 4 | 63 | 0.74 | 0.99 | 16 | empty |
| 5 | 54 | 0.74 | 0.99 | 15 | empty |
Interfaces
14 interfaces between chains.
- C–G · 1743 Ų buried · 24 hydrogen bonds · protein-protein
- D–H · 1728 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1646 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1642 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 594 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6WPA · Structure of AvaR1 bound to DNA half-site · the same entry in another collection · chain A against A, TM-score 1.00
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 Q82H41
- Elsewhere: RCSB PDB 6WPA · PDBe 6WPA · UniProt Q82H41
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