MolNFT v1 · #126647 · protein
Crystal structure of sdea-modified ubiquitin.
5M93 · Polyubiquitin-B: “Crystal structure of sdea-modified ubiquitin.”. X-ray diffraction, 2 ligands (RIB, SO4), 2 pockets (best druggability 0.44). MolNFT v1 #126647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M93
- Type
- protein
- Length
- 230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B
- UniProt
- P0CG47
- Ligands
- RIB, SO4
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyubiquitin-B | protein | 75 | 20% helix, 35% strand | P0CG47 |
| B | Polyubiquitin-B | protein | 77 | 23% helix, 38% strand | P0CG47 |
| C | Polyubiquitin-B | protein | 78 | 19% helix, 37% strand | P0CG47 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · ligand · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
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 | 153 | 0.44 | 0.75 | 29 | SO4 |
| 2 | 107 | 0.37 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 683 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5M93 · Crystal structure of SdeA-modified 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 P0CG47
- Elsewhere: RCSB PDB 5M93 · PDBe 5M93 · UniProt P0CG47
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