MolNFT v1 · #63913 · protein

Crystal structure of hapten complex of catalytic elimination antibody 13G5 (GLU(L39)ALA mutant)

3FO1 · Catalytic antibody Fab 13G5 kappa light chain chimera: “Crystal structure of hapten complex of catalytic elimination antibody 13G5 (GLU(L39)ALA mutant)”. X-ray diffraction, 1 ligand (BZH), 8 pockets (best druggability 0.75). MolNFT…

PDB: 3FO1
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic antibody Fab 13G5 kappa light chain chimera; Catalytic antibody Fab 13G5 IGG2B…
Ligands: BZH
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Catalytic antibody Fab 13G5 kappa light chain chimera	protein	216	6% helix, 52% strand	—
H	Catalytic antibody Fab 13G5 IGG2B heavy chain chimera	protein	216	6% helix, 51% strand	—
B	Catalytic antibody Fab 13G5 IGG2B heavy chain chimera	protein	214	7% helix, 51% strand	—

Ligands and binding sites

BZH · 5-[(2-amino-1H-benzimidazol-6-yl)amino]-5-oxopentanoic acid · ligand · 2 copies · chains L, H, A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	483	0.75	0.83	60	empty
2	353	0.69	0.82	48	empty
3	92	0.64	0.90	23	BZH
4	53	0.63	0.94	16	empty
5	85	0.61	0.88	24	BZH

Interfaces

6 interfaces between chains.

L–H · 1861 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1818 Å² buried · 16 hydrogen bonds · protein-protein
H–B · 488 Å² buried · 5 hydrogen bonds · protein-protein
L–A · 272 Å² buried · 1 hydrogen bond · protein-protein
L–B · 38 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3FO1 · Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Ala… · 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 3FO1 · PDBe 3FO1

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