Research workbench
Crystal structure of H. polymorpha ubiquitin conjugating enzyme PEX4P in complex with soluble domain of PEX22P
Analyse Crystal structure of H. polymorpha ubiquitin conjugating enzyme PEX4P in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NKZ
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2-21 kda; Peroxin 22
- EC
- 2.3.2.23
- UniProt
- O60015, A2T0X6
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-conjugating enzyme E2-21 kda (EC 2.3.2.23) | protein | 182 | 36% helix, 17% strand | O60015 |
| D | Peroxin 22 | protein | 105 | 35% helix, 17% strand | A2T0X6 |
| C | Peroxin 22 | protein | 105 | 38% helix, 17% strand | A2T0X6 |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.75 | 0.81 | 67 | empty |
| 2 | 147 | 0.54 | 0.81 | 22 | empty |
| 3 | 66 | 0.49 | 0.84 | 15 | empty |
| 4 | 106 | 0.49 | 0.80 | 19 | empty |
| 5 | 101 | 0.39 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 816 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 789 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 742 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NKZ · Crystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O60015 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2-21 kda (O60015) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O60015
- Every structure of UniProt A2T0X6
- Elsewhere: RCSB PDB 5NKZ · PDBe 5NKZ · UniProt O60015 · UniProt A2T0X6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.