MolNFT v1 · #128255 · protein
Crystal structure of H. polymorpha ubiquitin conjugating enzyme PEX4P in complex with soluble domain of PEX22P
5NKZ · Ubiquitin-conjugating enzyme E2-21 kda: “Crystal structure of H. polymorpha ubiquitin conjugating enzyme PEX4P in complex with soluble domain of PEX22P”. X-ray diffraction, 11 pockets (best druggability 0.75). MolNFT v1 #128255 on…
- 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
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