MolNFT v1 · #15916 · protein

Cocaine hydrolytic antibody 15A10

1NJ9 · Immunoglobulin variable chain: “Cocaine hydrolytic antibody 15A10”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.68). MolNFT v1 #15916 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NJ9
Type: protein
Length: 854 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin variable chain; Immunoglobulin heavy chain
Ligands: NA
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Immunoglobulin variable chain	protein	212	7% helix, 51% strand	—
H, B	Immunoglobulin heavy chain	protein	215	6% helix, 52% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 8 copies · chains L, H, A, B

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

Pockets

10 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	534	0.68	0.78	59	empty
2	335	0.53	0.74	48	empty
3	228	0.52	0.76	33	empty
4	139	0.42	0.75	20	empty
5	112	0.40	0.76	20	empty

Interfaces

5 interfaces between chains.

A–B · 1712 Å² buried · 10 hydrogen bonds · protein-protein
L–H · 1685 Å² buried · 14 hydrogen bonds · protein-protein
H–B · 393 Å² buried · 5 hydrogen bonds · protein-protein
L–B · 109 Å² buried · 1 hydrogen bond · protein-protein
H–A · 82 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1NJ9 · Cocaine hydrolytic antibody 15A10 · 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 1NJ9 · PDBe 1NJ9

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