Research workbench
X-ray structure of selenomethionyl gene product from arabidopsis thaliana AT5G02240 in space group P21212
Analyse X-ray structure of selenomethionyl gene product from arabidopsis thaliana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YBM
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unknown protein AT5G02240
- UniProt
- Q94EG6
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Unknown protein AT5G02240 | protein | 243 | 36% helix, 22% 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 | 427 | 0.67 | 0.79 | 43 | NAP |
| 2 | 422 | 0.66 | 0.79 | 47 | NAP |
| 3 | 414 | 0.61 | 0.76 | 33 | empty |
| 4 | 83 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 224 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1YBM · X-ray structure of selenomethionyl gene product from Arabidopsis thaliana at5g02240 in… · the same entry in another collection · chain B against B, 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 0.99
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 1YBM · PDBe 1YBM · UniProt Q94EG6
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