Research workbench
Crystal structure of ubiquitin conjugating enzyme E2 from plasmodium falciparum
Analyse Crystal structure of ubiquitin conjugating enzyme E2 from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H2Y
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme
- EC
- 6.3.2.19
- UniProt
- Q8IDP1
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme (EC 6.3.2.19) | protein | 133 | 22% helix, 19% strand | Q8IDP1 |
| B, C | Ubiquitin-conjugating enzyme (EC 6.3.2.19) | protein | 113 | 25% helix, 21% strand | Q8IDP1 |
| D | Ubiquitin-conjugating enzyme (EC 6.3.2.19) | protein | 112 | 24% helix, 23% strand | Q8IDP1 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.81 | 0.83 | 91 | empty |
| 2 | 149 | 0.52 | 0.80 | 28 | empty |
| 3 | 128 | 0.50 | 0.80 | 24 | empty |
| 4 | 130 | 0.46 | 0.77 | 17 | empty |
| 5 | 66 | 0.40 | 0.80 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 680 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 620 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2H2Y · Crystal structure of ubiquitin conjugating enzyme E2 from plasmodium falciparum · 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 Q8IDP1
- Elsewhere: RCSB PDB 2H2Y · PDBe 2H2Y · UniProt Q8IDP1
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