MolNFT v1 · #139804 · protein

Catalytic antibody 7B9

5XQW · Fab fragment of catalytic antibody 7B9, light chain: “Catalytic antibody 7B9”. X-ray diffraction, 1 ligand (8EU), 5 pockets (best druggability 0.66). MolNFT v1 #139804 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XQW
Type: protein
Length: 421 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment of catalytic antibody 7B9, light chain; Fab fragment of catalytic antibody…
Ligands: 8EU
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab fragment of catalytic antibody 7B9, light chain	protein	211	6% helix, 54% strand	—
H	Fab fragment of catalytic antibody 7B9, heavy chain	protein	210	6% helix, 56% strand	—

Ligands and binding sites

8EU · ethyl-[(4-nitrophenyl)methoxy]phosphinic acid · ligand · chains L, H

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	115	0.66	0.89	30	8EU
2	50	0.53	0.89	20	empty
3	208	0.47	0.74	43	empty
4	117	0.38	0.74	19	empty
5	58	0.26	0.72	16	empty

Interfaces

1 interface between chains.

L–H · 1677 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5XQW · Catalytic antibody 7B9 · 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 5XQW · PDBe 5XQW

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