MolNFT v1 · #154878 · protein
The crystal structure of the JACKDAW/IDD10 bound to the homodimeric SCL3
6KPB · Scarecrow-like protein 3: “The crystal structure of the JACKDAW/IDD10 bound to the homodimeric SCL3”. X-ray diffraction, 2 pockets (best druggability 0.71). MolNFT v1 #154878 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6KPB
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scarecrow-like protein 3; Peptide from zinc finger protein jackdaw
- UniProt
- Q9LPR8, Q700D2
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Scarecrow-like protein 3 | protein | 378 | 54% helix, 16% strand | Q9LPR8 |
| B | Peptide from zinc finger protein jackdaw | protein | 14 | 79% helix, 0% strand | Q700D2 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.71 | 0.80 | 43 | empty |
| 2 | 69 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- C–B · 460 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KPB · The crystal structure of the JACKDAW/IDD10 bound to the homodimeric SCL3 · the same entry in another collection · chain C against C, TM-score 1.00
- Q9LPR8 · AlphaFold monomer V2.0 prediction for scarecrow-like protein 3 (Q9LPR8) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q700D2 · AlphaFold monomer V2.0 prediction for zinc finger protein jackdaw (Q700D2) · a predicted model of the same protein · chain B against A, TM-score 0.64
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 Q9LPR8
- Every structure of UniProt Q700D2
- Elsewhere: RCSB PDB 6KPB · PDBe 6KPB · UniProt Q9LPR8 · UniProt Q700D2
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