Research workbench
Structure of full-length human lambda-6A light chain jto in complex with urea stabilizer 20 [1-(2-(7-(diethylamino)-4-methyl-2-oxo-2H- chromen-3-YL)ETHYL)-3-(pyridin-3-YLMETHYL)UREA]
Analyse Structure of full-length human lambda-6A light chain jto in complex with urea… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RTP
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jto light chain
- Ligands
- NY9, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Jto light chain | protein | 215 | 7% helix, 47% strand | — |
Ligands and binding sites
- NY9 · N-{2-[7-(diethylamino)-4-methyl-2-oxo-2H-1-benzopyran-3-yl]ethyl}-N'-[(pyridin-3-yl)methyl]urea · ligand · chains A, B
- PO4 · Phosphate ion · ion · 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 | 505 | 0.62 | 0.76 | 55 | empty |
| 2 | 293 | 0.62 | 0.79 | 39 | NY9 |
| 3 | 372 | 0.58 | 0.76 | 69 | empty |
| 4 | 141 | 0.39 | 0.73 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1639 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7RTP · Structure of full-length human lambda-6A light chain JTO in complex with urea stabilizer… · 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 7RTP · PDBe 7RTP
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