Research workbench
Structural analysis of leishmania major ubiquitin conjugating enzyme E2
Analyse Structural analysis of leishmania major ubiquitin conjugating enzyme E2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YF9
- Type
- protein
- Length
- 477 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carrier protein 4
- UniProt
- Q4Q5L3
- Ligands
- CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carrier protein 4 | protein | 158 | 41% helix, 16% strand | Q4Q5L3 |
| B | Ubiquitin carrier protein 4 | protein | 160 | 41% helix, 16% strand | Q4Q5L3 |
| C | Ubiquitin carrier protein 4 | protein | 159 | 40% helix, 15% strand | Q4Q5L3 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.77 | 0.80 | 74 | CL |
| 2 | 69 | 0.44 | 0.81 | 15 | empty |
| 3 | 50 | 0.38 | 0.81 | 15 | empty |
| 4 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 660 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 644 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1YF9 · Structural analysis of Leishmania major ubiquitin conjugating enzyme E2 · 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 Q4Q5L3
- Elsewhere: RCSB PDB 1YF9 · PDBe 1YF9 · UniProt Q4Q5L3
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