MolNFT v1 · #163283 · protein + DNA
Wus-hd bound to tgaa DNA
6RYD · Protein wuschel: “Wus-hd bound to tgaa DNA”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.72). MolNFT v1 #163283 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RYD
- Type
- protein + DNA
- Length
- 318 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein wuschel; DNA (5'-D(*AP*GP*TP*GP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*CP*G)- 3'); DNA…
- UniProt
- Q9SB92
- Ligands
- MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein wuschel | protein | 69 | 65% helix, 0% strand | Q9SB92 |
| B | Protein wuschel | protein | 59 | 69% helix, 0% strand | Q9SB92 |
| C, G | DNA (5'-D(*AP*GP*TP*GP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*CP*G)- 3') | dna | 16 | — | — |
| D, H | DNA (5'-D(*CP*GP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*CP*AP*CP*T)- 3') | dna | 16 | — | — |
| E | Protein wuschel | protein | 68 | 63% helix, 0% strand | Q9SB92 |
| F | Protein wuschel | protein | 58 | 66% helix, 0% strand | Q9SB92 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.72 | 0.76 | 77 | empty |
| 2 | 88 | 0.58 | 0.87 | 20 | empty |
| 3 | 272 | 0.57 | 0.78 | 27 | empty |
| 4 | 53 | 0.54 | 0.89 | 13 | empty |
| 5 | 179 | 0.51 | 0.78 | 20 | empty |
Interfaces
16 interfaces between chains.
- C–D · 732 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- G–H · 724 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- F–G · 521 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–G · 493 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 493 Ų buried · 9 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 6RYD · PDBe 6RYD · UniProt Q9SB92
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