MolNFT v1 · #109335 · protein
SER65 phosphorylated ubiquitin, major conformation
4WZP: “SER65 phosphorylated ubiquitin, major conformation”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.70). MolNFT v1 #109335 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WZP
- Type
- protein
- Length
- 587 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P0CG47
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ubiquitin | protein | 74 | 24% helix, 35% strand | P0CG47 |
| D | Ubiquitin | protein | 75 | 24% helix, 35% strand | P0CG47 |
| E | Ubiquitin | protein | 71 | 25% helix, 37% strand | P0CG47 |
| F, H | Ubiquitin | protein | 73 | 25% helix, 34% strand | P0CG47 |
| G | Ubiquitin | protein | 73 | 25% helix, 34% strand | P0CG47 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, F, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.70 | 0.75 | 59 | empty |
| 2 | 763 | 0.66 | 0.74 | 75 | empty |
| 3 | 293 | 0.65 | 0.81 | 43 | empty |
| 4 | 78 | 0.47 | 0.82 | 16 | empty |
| 5 | 77 | 0.32 | 0.74 | 21 | empty |
Interfaces
15 interfaces between chains.
- C–D · 660 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 558 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 484 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 462 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 4WZP · Ser65 phosphorylated ubiquitin, major conformation · the same entry in another collection · chain G against G, 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 P0CG47
- Elsewhere: RCSB PDB 4WZP · PDBe 4WZP · UniProt P0CG47
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