MolNFT v1 · #168085 · protein
Structure of full-length human lambda-6A light chain jto in complex with hydantoin stabilizer
6W4Y · Jto light chain: “Structure of full-length human lambda-6A light chain jto in complex with hydantoin stabilizer”. X-ray diffraction, 2 ligands (7ZW, PO4), 7 pockets (best druggability 0.64). MolNFT v1 #168085 on GenesisL1: 3D…
- PDB
- 6W4Y
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jto light chain
- Ligands
- 7ZW, PO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Jto light chain | protein | 215 | 9% helix, 48% strand | — |
Ligands and binding sites
- 7ZW · 2-[(4~{R})-4-(2-methylpropyl)-2,5-bis(oxidanylidene) imidazolidin-1-yl]-~{N}-[4-(trifluoromethyl) phenyl]ethanamide · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.64 | 0.75 | 60 | GOL |
| 2 | 322 | 0.56 | 0.76 | 50 | empty |
| 3 | 58 | 0.54 | 0.87 | 15 | 7ZW |
| 4 | 76 | 0.42 | 0.80 | 29 | empty |
| 5 | 85 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1792 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6W4Y · Structure of full-length human lambda-6A light chain JTO in complex with hydantoin… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6W4Y · PDBe 6W4Y
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