Research workbench
Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin
Analyse Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z9S
- Type
- protein
- Length
- 300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-40S ribosomal protein S27A
- UniProt
- P62992
- Ligands
- SCN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ubiquitin-40S ribosomal protein S27A | protein | 75 | 20% helix, 33% strand | P62992 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 9 copies · chains A, D, B, C
- MLA · Malonic acid · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.55 | 0.74 | 56 | SCN, MLA |
| 2 | 72 | 0.39 | 0.79 | 14 | SCN |
| 3 | 83 | 0.39 | 0.78 | 17 | MLA |
| 4 | 68 | 0.38 | 0.79 | 16 | MLA |
| 5 | 50 | 0.37 | 0.81 | 16 | SCN |
Interfaces
4 interfaces between chains.
- B–C · 312 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 299 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 279 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4Z9S · Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P62992
- Elsewhere: RCSB PDB 4Z9S · PDBe 4Z9S · UniProt P62992
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.