Research workbench
Crystal structure of human MMS2/UBC13 - bay 11-7082
Analyse Crystal structure of human MMS2/UBC13 - bay 11-7082 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ONN
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 variant 2; Ubiquitin-conjugating enzyme E2 N
- EC
- 6.3.2.19
- UniProt
- Q15819, P61088
- Ligands
- BY1
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 variant 2 | protein | 140 | 23% helix, 20% strand | Q15819 |
| B | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 149 | 33% helix, 18% strand | P61088 |
Ligands and binding sites
- BY1 · 3-[(4-methylphenyl)sulfonyl]prop-2-enenitrile · ligand · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 148 | 0.50 | 0.78 | 21 | BY1, GOL |
| 2 | 76 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 801 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ONN · Crystal structure of human Mms2/Ubc13 - BAY 11-7082 · the same entry in another collection · chain A against A, TM-score 1.00
- Q15819 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 2 (Q15819) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q15819
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 4ONN · PDBe 4ONN · UniProt Q15819 · UniProt P61088
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