Research workbench
MMS2/UBC13~UBIQUITIN
Analyse MMS2/UBC13~UBIQUITIN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GMI
- Type
- protein
- Length
- 363 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 13; Ubiquitin-conjugating enzyme variant MMS2; Ubiquitin
- EC
- 6.3.2.19
- UniProt
- P52490, P53152, Q867C3
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 13 (EC 6.3.2.19) | protein | 152 | 34% helix, 22% strand | P52490 |
| B | Ubiquitin-conjugating enzyme variant MMS2 | protein | 135 | 17% helix, 21% strand | P53152 |
| C | Ubiquitin | protein | 76 | 24% helix, 32% strand | Q867C3 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.74 | 0.78 | 61 | empty |
| 2 | 77 | 0.35 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 702 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GMI · Mms2/Ubc13~Ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P52490 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 13 (P52490) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P53152 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme variant MMS2 (P53152) · 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 P52490
- Every structure of UniProt P53152
- Every structure of UniProt Q867C3
- Elsewhere: RCSB PDB 2GMI · PDBe 2GMI · UniProt P52490 · UniProt P53152 · UniProt Q867C3
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