MolNFT v1 · #122153 · protein
WD40 domain of human E3 ubiquitin ligase COP1 (RFWD2) bound to peptide from TRIB1
5IGQ · E3 ubiquitin-protein ligase RFWD2: “WD40 domain of human E3 ubiquitin ligase COP1 (RFWD2) bound to peptide from TRIB1”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #122153 on GenesisL1: 3D structure, binding…
- 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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