Research workbench

Anti-cocaine antibody M82G2 complexed with norbenzoylecgonine

Analyse Anti-cocaine antibody M82G2 complexed with norbenzoylecgonine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RIU
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab M82G2, light chain; Fab M82G2, heavy chain
Ligands: RBE
Pockets: 6 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab M82G2, light chain	protein	218	6% helix, 50% strand	—
H	Fab M82G2, heavy chain	protein	220	10% helix, 52% strand	—

Ligands and binding sites

RBE · 3-(benzoyloxy)-8-aza-bicyclo[3.2.1]octane-2-carboxylic acid · ligand · chains L, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.46	0.74	35	empty
2	103	0.44	0.78	16	RBE
3	136	0.41	0.75	22	empty
4	91	0.32	0.73	18	empty
5	60	0.29	0.74	13	empty

Interfaces

1 interface between chains.

L–H · 1755 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1RIU · Anti-Cocaine Antibody M82G2 Complexed With Norbenzoylecgonine · the same entry in another collection · chain L against L, 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 1RIU · PDBe 1RIU

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