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Catalytic antibody complex

Analyse Catalytic antibody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YEJ
Type: protein
Length: 441 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (ig antibody D2.3 (light chain)); Protein (ig antibody D2.3 (heavy chain))
Ligands: PNF, ZN
Pockets: 3 · best druggability 0.62

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Protein (ig antibody D2.3 (light chain))	protein	219	5% helix, 52% strand	—
H	Protein (ig antibody D2.3 (heavy chain))	protein	222	8% helix, 52% strand	—

Ligands and binding sites

PNF · 6-{4-[hydroxy-(4-nitro-phenoxy)-phosphoryl]-butyrylamino}-hexanoic acid · ligand · chains L, H
ZN · Zinc ion · metal · 7 copies · chains L, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.62	0.84	25	PNF
2	180	0.41	0.73	35	empty
3	62	0.35	0.78	12	empty

Interfaces

1 interface between chains.

L–H · 2080 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1YEJ · Catalytic antibody complex · 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 1YEJ · PDBe 1YEJ

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