Research workbench
X-ray structure of the non-covalent complex between UBCH5A and ubiquitin
Analyse X-ray structure of the non-covalent complex between UBCH5A and ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PTF
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D1; Polyubiquitin-B
- EC
- 6.3.2.19
- UniProt
- P51668, P0CG47
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 153 | 39% helix, 17% strand | P51668 |
| B | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 152 | 39% helix, 18% strand | P51668 |
| C | Polyubiquitin-B | protein | 73 | 25% helix, 34% strand | P0CG47 |
| D | Polyubiquitin-B | protein | 74 | 20% helix, 36% strand | P0CG47 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.65 | 0.84 | 34 | empty |
| 2 | 160 | 0.56 | 0.81 | 26 | empty |
| 3 | 144 | 0.55 | 0.81 | 25 | empty |
| 4 | 186 | 0.52 | 0.78 | 24 | empty |
| 5 | 112 | 0.50 | 0.80 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–C · 665 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 626 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 483 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 134 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3PTF · X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P51668
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 3PTF · PDBe 3PTF · UniProt P51668 · UniProt P0CG47
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