MolNFT v1 · #163286 · protein + DNA
Wus-hd bound to G-box DNA
6RYI · Protein wuschel: “Wus-hd bound to G-box DNA”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #163286 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RYI
- Type
- protein + DNA
- Length
- 359 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein wuschel; DNA (5'- D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3'); DNA…
- UniProt
- Q9SB92
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein wuschel | protein | 59 | 66% helix, 0% strand | Q9SB92 |
| C, D, E | Protein wuschel | protein | 60 | 68% helix, 0% strand | Q9SB92 |
| F | DNA (5'- D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3') | dna | 16 | — | — |
| G | DNA (5'- D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3') | dna | 16 | — | — |
| H | DNA (5'- D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3') | dna | 15 | — | — |
| I | DNA (5'- D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3') | dna | 14 | — | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.73 | 0.78 | 61 | empty |
| 2 | 480 | 0.70 | 0.81 | 35 | empty |
| 3 | 142 | 0.48 | 0.78 | 17 | empty |
| 4 | 67 | 0.41 | 0.80 | 12 | empty |
| 5 | 126 | 0.38 | 0.75 | 16 | empty |
Interfaces
16 interfaces between chains.
- F–G · 724 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- H–I · 670 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- D–I · 483 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–F · 477 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–G · 460 Ų buried · 11 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 Q9SB92
- Elsewhere: RCSB PDB 6RYI · PDBe 6RYI · UniProt Q9SB92
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