MolNFT v1 · #156814 · protein

Structure of full-length human lambda-6A light chain jto in complex with coumarin 1

6MG5: “Structure of full-length human lambda-6A light chain jto in complex with coumarin 1”. X-ray diffraction, 2 ligands (6ZW, PO4), 6 pockets (best druggability 0.64). MolNFT v1 #156814 on GenesisL1: 3D structure, binding sites and…

PDB: 6MG5
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain jto
Ligands: 6ZW, PO4
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Light chain jto	protein	215	7% helix, 50% strand	—

Ligands and binding sites

6ZW · 7-(diethylamino)-4-methyl-2H-1-benzopyran-2-one · 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

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	565	0.64	0.76	49	empty
2	285	0.63	0.80	39	6ZW
3	220	0.51	0.76	28	empty
4	90	0.38	0.76	25	empty
5	82	0.34	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 1726 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6MG5 · Structure of full-length human lambda-6A light chain JTO in complex with coumarin 1 · 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 6MG5 · PDBe 6MG5

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