Research workbench
Structure of ubiquitin fold protein R767E mutant
Analyse Structure of ubiquitin fold protein R767E mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5G
- Type
- protein
- Length
- 497 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Axin-1
- UniProt
- O70239
- Ligands
- HG
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Axin-1 | protein | 83 | 6% helix, 46% strand | O70239 |
| B | Axin-1 | protein | 85 | 6% helix, 45% strand | O70239 |
| E | Axin-1 | protein | 80 | 6% helix, 44% strand | O70239 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.37 | 0.76 | 20 | empty |
| 2 | 95 | 0.37 | 0.75 | 25 | empty |
| 3 | 76 | 0.32 | 0.74 | 22 | empty |
| 4 | 50 | 0.24 | 0.72 | 12 | empty |
Interfaces
5 interfaces between chains.
- E–F · 854 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 838 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 815 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 697 Ų buried · 10 hydrogen bonds · protein-protein
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 O70239
- Elsewhere: RCSB PDB 2D5G · PDBe 2D5G · UniProt O70239
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