MolNFT v1 · #181165 · protein
Structure of full-length human lambda-6A light chain jto in complex with stabilizer 36 [3-(2-(7-(diethylamino)-4-methyl-2-oxo-2H-chromen- 3-YL)ETHYL)-8-(1H-imidazole-4-carbonyl)-1,3,8-TRIAZASPIRO[4.5]DECANE- 2,4-dione]
7LMP · Jto light chain: “Structure of full-length human lambda-6A light chain jto in complex with stabilizer 36…”. X-ray diffraction, 2 ligands (NY6, PO4), 4 pockets (best druggability 0.64). MolNFT v1 #181165 on GenesisL1: 3D structure…
- PDB
- 7LMP
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jto light chain
- Ligands
- NY6, PO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Jto light chain | protein | 215 | 7% helix, 48% strand | — |
Ligands and binding sites
- NY6 · 3-[2-[7-(diethylamino)-4-methyl-2-oxidanylidene-chromen-3-yl]ethyl]-8-(1~{H}-imidazol-5-ylcarbonyl)-1, 3,8-triazaspiro[4.5]decane-2,4-dione · 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 | 597 | 0.64 | 0.75 | 57 | empty |
| 2 | 165 | 0.58 | 0.81 | 26 | NY6 |
| 3 | 278 | 0.52 | 0.75 | 40 | empty |
| 4 | 81 | 0.32 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1718 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7LMP · Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 36… · 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 7LMP · PDBe 7LMP
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