Research workbench
The crystal structure of the rangdp-NUP153ZNF2 complex
Analyse The crystal structure of the rangdp-NUP153ZNF2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CH5
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Fragment of nuclear pore complex protein NUP153
- UniProt
- P62826, P49791
- Ligands
- GDP, MG, ZN, SO4
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 193 | 33% helix, 28% strand | P62826 |
| B | Fragment of nuclear pore complex protein NUP153 | protein | 37 | 0% helix, 16% strand | P49791 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.40 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3CH5 · The crystal structure of the RanGDP-Nup153ZnF2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P49791 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP153 (P49791) · a predicted model of the same protein · chain B against A, TM-score 0.77
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 P62826
- Every structure of UniProt P49791
- Elsewhere: RCSB PDB 3CH5 · PDBe 3CH5 · UniProt P62826 · UniProt P49791
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