Research workbench

Catalytic elimination antibody 34E4 in complex with hapten

Analyse Catalytic elimination antibody 34E4 in complex with hapten in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Y0L
Type: protein
Length: 1,768 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic antibody Fab 34E4 light chain; Catalytic antibody Fab 34E4 heavy chain
Ligands: HAN, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A, C, E	Catalytic antibody Fab 34E4 light chain	protein	216	7% helix, 52% strand	—
H, B, D, F	Catalytic antibody Fab 34E4 heavy chain	protein	226	10% helix, 53% strand	—

Ligands and binding sites

HAN · 2-amino-5,6-dimethyl-benzimidazole-1-pentanoic acid · ligand · 4 copies · chains L, H, A, B, C, D, E, F
CL · Chloride ion · ion · chains E

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.80	0.84	71	empty
2	823	0.77	0.81	88	empty
3	1191	0.76	0.79	121	empty
4	343	0.71	0.84	44	empty
5	258	0.66	0.83	39	empty

Interfaces

17 interfaces between chains.

C–D · 2057 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1972 Å² buried · 9 hydrogen bonds · protein-protein
L–H · 1940 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1934 Å² buried · 13 hydrogen bonds · protein-protein
H–B · 1088 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

1Y0L · Catalytic elimination antibody 34E4 in complex with hapten · 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 1Y0L · PDBe 1Y0L

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