Research workbench
Crystal structure of KAP121P bound to rangtp
Analyse Crystal structure of KAP121P bound to rangtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W3Z
- Type
- protein
- Length
- 1,184 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Importin subunit beta-3; GTP-binding nuclear protein ran
- UniProt
- P32337, P62825
- Ligands
- GTP, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Importin subunit beta-3 | protein | 1013 | 76% helix, 1% strand | P32337 |
| B | GTP-binding nuclear protein ran | protein | 171 | 29% helix, 27% strand | P62825 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.78 | 0.80 | 96 | empty |
| 2 | 290 | 0.65 | 0.81 | 36 | MG, GTP |
| 3 | 246 | 0.51 | 0.75 | 32 | empty |
| 4 | 69 | 0.42 | 0.80 | 13 | empty |
| 5 | 64 | 0.41 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1668 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3W3Z · Crystal structure of Kap121p bound to RanGTP · the same entry in another collection · chain A against A, TM-score 1.00
- P62825 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein ran (P62825) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.63
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 P62825
- Elsewhere: RCSB PDB 3W3Z · PDBe 3W3Z · UniProt P32337 · UniProt P62825
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