Research workbench
APC11-ubv shows role of noncovalent ring-ubiquitin interactions in processive multiubiquitination and ubiquitin chain elongation by APC/C
Analyse APC11-ubv shows role of noncovalent ring-ubiquitin interactions in processive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JG6
- Type
- protein
- Length
- 279 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase-promoting complex subunit 11; Polyubiquitin-B
- UniProt
- Q9NYG5, P0CG47
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaphase-promoting complex subunit 11 | protein | 61 | 16% helix, 20% strand | Q9NYG5 |
| B | Polyubiquitin-B | protein | 77 | 23% helix, 36% strand | P0CG47 |
| C | Polyubiquitin-B | protein | 75 | 24% helix, 35% strand | P0CG47 |
| D | Anaphase-promoting complex subunit 11 | protein | 66 | 15% helix, 18% strand | Q9NYG5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.34 | 0.74 | 19 | empty |
| 2 | 58 | 0.31 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 703 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 696 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JG6 · APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NYG5 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 11 (Q9NYG5) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9NYG5
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5JG6 · PDBe 5JG6 · UniProt Q9NYG5 · UniProt P0CG47
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