Research workbench
Conjugate of the hect domain of HUWE1 with ubiquitin
Analyse Conjugate of the hect domain of HUWE1 with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XZ1
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hect, uba and wwe domain containing 1, isoform CRA_A; Polyubiquitin-B
- UniProt
- A0A024R9Y3, P0CG47
- Ligands
- AYE, PO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hect, uba and wwe domain containing 1, isoform CRA_A | protein | 384 | 49% helix, 13% strand | A0A024R9Y3 |
| C, D | Polyubiquitin-B | protein | 75 | 24% helix, 35% strand | P0CG47 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, C, B, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.82 | 0.83 | 93 | empty |
| 2 | 138 | 0.64 | 0.87 | 32 | empty |
| 3 | 149 | 0.62 | 0.85 | 26 | empty |
| 4 | 239 | 0.54 | 0.77 | 26 | empty |
| 5 | 205 | 0.53 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 940 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 930 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6XZ1 · Conjugate of the HECT domain of HUWE1 with ubiquitin · the same entry in another collection · chain A against A, 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 A0A024R9Y3
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6XZ1 · PDBe 6XZ1 · UniProt A0A024R9Y3 · UniProt P0CG47
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