Research workbench
S. pombe UBC7/U7BR complex
Analyse S. pombe UBC7/U7BR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OP8
- Type
- protein
- Length
- 209 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2-18 kda; Cue domain-containing protein 4, mitochondrial
- EC
- 2.3.2.23
- UniProt
- O00102, P87238
- Ligands
- MG, NA
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2-18 kda (EC 2.3.2.23) | protein | 167 | 37% helix, 15% strand | O00102 |
| B | Cue domain-containing protein 4, mitochondrial | protein | 42 | 76% helix, 0% strand | P87238 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.38 | 0.77 | 16 | empty |
| 2 | 54 | 0.35 | 0.79 | 16 | empty |
| 3 | 61 | 0.26 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1303 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6OP8 · S. pombe Ubc7/U7BR complex · the same entry in another collection · chain A against A, TM-score 1.00
- O00102 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2-18 kda (O00102) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P87238 · AlphaFold monomer V2.0 prediction for cue domain-containing protein 4, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 O00102
- Every structure of UniProt P87238
- Elsewhere: RCSB PDB 6OP8 · PDBe 6OP8 · UniProt O00102 · UniProt P87238
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