MolNFT v1 · #62254 · protein
KAP95P binding induces the switch loops of rangdp to adopt the GTP- bound conformation: implications for nuclear import complex assembly dynamics
3EA5 · GTP-binding nuclear protein ran: “KAP95P binding induces the switch loops of rangdp to adopt the GTP- bound conformation: implications for…”. X-ray diffraction, 2 ligands (GDP, MG), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3EA5
- Type
- protein
- Length
- 2,051 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Importin subunit beta-1
- UniProt
- P62826, Q06142
- Ligands
- GDP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 174 | 28% helix, 27% strand | P62826 |
| B | Importin subunit beta-1 | protein | 859 | 78% helix, 0% strand | Q06142 |
| C | GTP-binding nuclear protein ran | protein | 169 | 27% helix, 27% strand | P62826 |
| D | Importin subunit beta-1 | protein | 849 | 78% helix, 0% strand | Q06142 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.82 | 0.84 | 63 | empty |
| 2 | 608 | 0.78 | 0.84 | 46 | empty |
| 3 | 693 | 0.69 | 0.77 | 49 | empty |
| 4 | 338 | 0.69 | 0.83 | 51 | empty |
| 5 | 230 | 0.68 | 0.85 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2432 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2391 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 2217 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EA5 · Kap95p Binding Induces the Switch Loops of RanGDP to adopt the GTP-bound Conformation… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06142 · AlphaFold monomer V2.0 prediction for importin subunit beta-1 (Q06142) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 Q06142
- Elsewhere: RCSB PDB 3EA5 · PDBe 3EA5 · UniProt P62826 · UniProt Q06142
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