Research workbench
Rice IMPORTIN_ALPHA : VIRD2NLS complex
Analyse Rice IMPORTIN_ALPHA : VIRD2NLS complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BQK
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Importin subunit alpha-1A; T-DNA border endonuclease VIRD2
- EC
- 3.1.-.-
- UniProt
- Q71VM4, P18592
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Importin subunit alpha-1A | protein | 424 | 74% helix, 0% strand | Q71VM4 |
| B | Importin subunit alpha-1A | protein | 422 | 75% helix, 0% strand | Q71VM4 |
| C | T-DNA border endonuclease VIRD2 (EC 3.1.-.-) | protein | 12 | 0% helix, 0% strand | P18592 |
| D | T-DNA border endonuclease VIRD2 (EC 3.1.-.-) | protein | 14 | 0% helix, 0% strand | P18592 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 154 | 0.53 | 0.80 | 23 | empty |
| 2 | 177 | 0.44 | 0.74 | 28 | PEG |
| 3 | 55 | 0.31 | 0.76 | 14 | empty |
| 4 | 55 | 0.28 | 0.74 | 14 | PEG |
Interfaces
3 interfaces between chains.
- A–D · 1393 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 1243 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 655 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4BQK · rice importin_alpha : VirD2NLS complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q71VM4 · AlphaFold monomer V2.0 prediction for importin subunit alpha-1A (Q71VM4) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P18592 · AlphaFold monomer V2.0 prediction for T-DNA border endonuclease VIRD2 (P18592) · a predicted model of the same protein · chain C against A, TM-score 0.33
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 Q71VM4
- Every structure of UniProt P18592
- Elsewhere: RCSB PDB 4BQK · PDBe 4BQK · UniProt Q71VM4 · UniProt P18592
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