Research workbench
Crystal structure of a UBE2S-ubiquitin conjugate
Analyse Crystal structure of a UBE2S-ubiquitin conjugate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BNB
- Type
- protein
- Length
- 852 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 S; Polyubiquitin-B
- EC
- 6.3.2.19
- UniProt
- Q16763, P0CG47
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-conjugating enzyme E2 S (EC 6.3.2.19) | protein | 150 | 41% helix, 16% strand | Q16763 |
| C | Ubiquitin-conjugating enzyme E2 S (EC 6.3.2.19) | protein | 148 | 39% helix, 18% strand | Q16763 |
| E | Polyubiquitin-B | protein | 76 | 24% helix, 28% strand | P0CG47 |
| F, G | Polyubiquitin-B | protein | 72 | 25% helix, 36% strand | P0CG47 |
| I | Polyubiquitin-B | protein | 68 | 22% helix, 25% strand | P0CG47 |
| D | Ubiquitin-conjugating enzyme E2 S (EC 6.3.2.19) | protein | 116 | 39% helix, 22% strand | Q16763 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.80 | 0.82 | 107 | empty |
| 2 | 278 | 0.68 | 0.83 | 32 | empty |
| 3 | 372 | 0.64 | 0.78 | 55 | empty |
| 4 | 278 | 0.55 | 0.76 | 41 | empty |
| 5 | 202 | 0.46 | 0.74 | 26 | empty |
Interfaces
12 interfaces between chains.
- B–F · 536 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 213 Ų buried · 1 hydrogen bond · protein-protein
- I–D · 205 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 177 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 Q16763
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5BNB · PDBe 5BNB · UniProt Q16763 · UniProt P0CG47
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