Research workbench
Ensemble refinement of the protein crystal structure of selenomethionyl gene product from arabidopsis thaliana AT5G02240 in space group P21212
Analyse Ensemble refinement of the protein crystal structure of selenomethionyl gene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q4B
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein AT5G02240
- UniProt
- Q94EG6
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein AT5G02240 | protein | 243 | 35% helix, 21% strand | Q94EG6 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.68 | 0.79 | 44 | NAP |
| 2 | 418 | 0.64 | 0.78 | 46 | NAP |
| 3 | 396 | 0.62 | 0.77 | 36 | empty |
| 4 | 63 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 220 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2Q4B · Ensemble refinement of the protein crystal structure of selenomethionyl gene product from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q94EG6 · AlphaFold monomer V2.0 prediction for uncharacterized protein AT5G02240 (Q94EG6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q94EG6
- Elsewhere: RCSB PDB 2Q4B · PDBe 2Q4B · UniProt Q94EG6
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