Research workbench
WD40 domain of human E3 ubiquitin ligase COP1 (RFWD2) bound to peptide from TRIB1
Analyse WD40 domain of human E3 ubiquitin ligase COP1 (RFWD2) bound to peptide from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IGQ
- Type
- protein
- Length
- 1,995 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RFWD2; Tribbles homolog 1
- EC
- 6.3.2.-
- UniProt
- Q8NHY2, Q96RU8
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | E3 ubiquitin-protein ligase RFWD2 (EC 6.3.2.-) | protein | 324 | 4% helix, 49% strand | Q8NHY2 |
| U | Tribbles homolog 1 | protein | 11 | 0% helix, 9% strand | Q96RU8 |
| V, W, X, Y, Z | Tribbles homolog 1 | protein | 8 | 0% helix, 13% strand | Q96RU8 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.74 | 0.84 | 49 | empty |
| 2 | 415 | 0.74 | 0.84 | 59 | empty |
| 3 | 431 | 0.74 | 0.83 | 51 | empty |
| 4 | 360 | 0.74 | 0.85 | 54 | empty |
| 5 | 422 | 0.73 | 0.83 | 49 | empty |
Interfaces
16 interfaces between chains.
- E–Y · 643 Ų buried · 9 hydrogen bonds · protein-protein
- A–U · 642 Ų buried · 5 hydrogen bonds · protein-protein
- C–W · 638 Ų buried · 8 hydrogen bonds · protein-protein
- B–V · 637 Ų buried · 8 hydrogen bonds · protein-protein
- F–Z · 634 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5IGQ · WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1 · the same entry in another collection · chain Z against Z, 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 Q8NHY2
- Every structure of UniProt Q96RU8
- Elsewhere: RCSB PDB 5IGQ · PDBe 5IGQ · UniProt Q8NHY2 · UniProt Q96RU8
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