MolNFT v1 · #128892 · protein
Crystal structure of unbranched mixed tri-ubiquitin chain containing K48 and K63 linkages.
5O44: “Crystal structure of unbranched mixed tri-ubiquitin chain containing K48 and K63 linkages.”. X-ray diffraction, 2 ligands (MG, SO4), 2 pockets (best druggability 0.38). MolNFT v1 #128892 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5O44
- Type
- protein
- Length
- 452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Polyubiquitin-B
- UniProt
- Q45TR8, P0CG47
- Ligands
- MG, SO4
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ubiquitin | protein | 76 | 25% helix, 28% strand | Q45TR8 |
| C, B | Polyubiquitin-B | protein | 74 | 26% helix, 35% strand | P0CG47 |
| D, F | Polyubiquitin-B | protein | 76 | 25% helix, 34% strand | P0CG47 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, D, E
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, D, F, B, E
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 | 74 | 0.38 | 0.78 | 17 | empty |
| 2 | 54 | 0.31 | 0.76 | 15 | empty |
Interfaces
8 interfaces between chains.
- C–D · 720 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 656 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 492 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 491 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 413 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 5O44 · Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages. · the same entry in another collection · chain B against B, 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 Q45TR8
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5O44 · PDBe 5O44 · UniProt Q45TR8 · UniProt P0CG47
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