Research workbench
Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana AT5G06450
Analyse Ensemble refinement of the protein crystal structure of gene product from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q3S
- Type
- protein
- Length
- 1,200 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein AT5G06450
- UniProt
- Q9FNG3
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protein AT5G06450 | protein | 200 | 45% helix, 22% strand | Q9FNG3 |
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.69 | 0.80 | 42 | empty |
| 2 | 381 | 0.67 | 0.80 | 40 | empty |
| 3 | 399 | 0.67 | 0.80 | 36 | empty |
| 4 | 454 | 0.67 | 0.79 | 37 | empty |
| 5 | 294 | 0.65 | 0.81 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1598 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1433 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1430 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1426 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2Q3S · Ensemble refinement of the protein crystal structure of gene product from Arabidopsis… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9FNG3 · AlphaFold monomer V2.0 prediction for protein risc-interacting clearing 3'-5'… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9FNG3
- Elsewhere: RCSB PDB 2Q3S · PDBe 2Q3S · UniProt Q9FNG3
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