Research workbench
Crystal structure of the karyopherin KAP121P bound to the sumo protease ULP1P
Analyse Crystal structure of the karyopherin KAP121P bound to the sumo protease ULP1P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H2V
- Type
- protein
- Length
- 1,032 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Importin subunit beta-3; Ubiquitin-like-specific protease 1
- EC
- 3.4.22.68
- UniProt
- P32337, Q02724
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Importin subunit beta-3 | protein | 1027 | 75% helix, 1% strand | P32337 |
| B | Ubiquitin-like-specific protease 1 (EC 3.4.22.68) | protein | 5 | 0% helix, 0% strand | Q02724 |
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 | 258 | 0.61 | 0.80 | 43 | empty |
| 2 | 205 | 0.49 | 0.75 | 23 | empty |
| 3 | 53 | 0.34 | 0.78 | 14 | empty |
| 4 | 73 | 0.29 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5H2V · Crystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p · the same entry in another collection · chain A against A, TM-score 1.00
- P32337 · AlphaFold monomer V2.0 prediction for importin subunit beta-3 (P32337) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q02724 · AlphaFold monomer V2.0 prediction for ubiquitin-like-specific protease 1 (Q02724) · a predicted model of the same protein · chain B against A, TM-score 0.64
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 P32337
- Every structure of UniProt Q02724
- Elsewhere: RCSB PDB 5H2V · PDBe 5H2V · UniProt P32337 · UniProt Q02724
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