MolNFT v1 · #114144 · protein
The crystal structure of the heterodimer of short-root and scarecrow gras domains
5B3G · Protein scarecrow: “The crystal structure of the heterodimer of short-root and scarecrow gras domains”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.85). MolNFT v1 #114144 on GenesisL1: 3D structure, binding…
- PDB
- 5B3G
- Type
- protein
- Length
- 777 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein scarecrow; Protein short-root
- UniProt
- Q9M384, Q9SZF7
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein scarecrow | protein | 371 | 53% helix, 16% strand | Q9M384 |
| B | Protein short-root | protein | 406 | 53% helix, 16% strand | Q9SZF7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.85 | 0.86 | 89 | PEG |
| 2 | 170 | 0.82 | 0.97 | 30 | empty |
| 3 | 587 | 0.75 | 0.82 | 62 | PEG |
| 4 | 50 | 0.72 | 0.99 | 17 | empty |
| 5 | 186 | 0.50 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2163 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5B3G · The crystal structure of the heterodimer of SHORT-ROOT and SCARECROW GRAS domains · the same entry in another collection · chain A against A, TM-score 1.00
- Q9M384 · AlphaFold monomer V2.0 prediction for protein scarecrow (Q9M384) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q9SZF7 · AlphaFold monomer V2.0 prediction for protein short-root (Q9SZF7) · a predicted model of the same protein · chain B 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 Q9M384
- Every structure of UniProt Q9SZF7
- Elsewhere: RCSB PDB 5B3G · PDBe 5B3G · UniProt Q9M384 · UniProt Q9SZF7
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