Research workbench

Antibody GNC92H2 bound to ligand

Analyse Antibody GNC92H2 bound to ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I7Z
Type: protein
Length: 878 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chimera of ig kappa chain: human constant region and mouse variable region; Chimera of ig…
UniProt: P01834, P01857
Ligands: COC
Pockets: 11 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Chimera of ig kappa chain: human constant region and mouse variable region	protein	219	6% helix, 50% strand	P01834
B, D	Chimera of ig gamma-1 chain: human constant region and mouse variable region	protein	220	8% helix, 50% strand	P01857

Ligands and binding sites

COC · Cocaine · ligand · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	616	0.70	0.79	65	empty
2	755	0.69	0.76	63	empty
3	158	0.68	0.87	18	COC
4	137	0.66	0.88	19	COC
5	566	0.62	0.74	59	empty

Interfaces

6 interfaces between chains.

A–B · 2083 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2004 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 900 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 485 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 22 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

1I7Z · Antibody GNC92H2 bound to ligand · the same entry in another collection · chain A against A, TM-score 1.00
P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain A against A, TM-score 0.48

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01834
Every structure of UniProt P01857
Elsewhere: RCSB PDB 1I7Z · PDBe 1I7Z · UniProt P01834 · UniProt P01857

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