MolNFT v1 · #15703 · protein

Cationic cyclization antibody 4C6 in complex with benzoic acid

1NCW · Immunoglobulin IGG2A: “Cationic cyclization antibody 4C6 in complex with benzoic acid”. X-ray diffraction, 1 ligand (BEZ), 6 pockets (best druggability 0.66). MolNFT v1 #15703 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1NCW
Type: protein
Length: 441 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin IGG2A
Ligands: BEZ
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Immunoglobulin IGG2A	protein	219	6% helix, 52% strand	—
H	Immunoglobulin IGG2A	protein	222	8% helix, 52% strand	—

Ligands and binding sites

BEZ · Benzoic acid · ligand · chains L, H
GOL · Glycerol · additive · 4 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	137	0.66	0.87	28	BEZ
2	444	0.57	0.74	55	empty
3	78	0.52	0.85	24	GOL
4	116	0.39	0.75	23	empty
5	79	0.35	0.76	20	empty

Interfaces

1 interface between chains.

L–H · 2100 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1NCW · Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid · 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 1NCW · PDBe 1NCW

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