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Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal form

Analyse Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CFJ
Type: protein
Length: 1,756 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic antibody Fab 34E4 light chain fusion; Catalytic antibody Fab 34E4 heavy chain…
UniProt: Q8TCD0, A8K008
Ligands: SO4
Pockets: 19 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A, C, E	Catalytic antibody Fab 34E4 light chain fusion	protein	215	8% helix, 53% strand	Q8TCD0
H, B, D, F	Catalytic antibody Fab 34E4 heavy chain fusion	protein	224	9% helix, 51% strand	A8K008

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains H, D
GOL · Glycerol · additive · 3 copies · chains L, H, A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1157	0.79	0.81	109	empty
2	995	0.79	0.80	102	empty
3	457	0.71	0.81	48	empty
4	822	0.68	0.75	78	empty
5	301	0.63	0.80	47	empty

Interfaces

13 interfaces between chains.

E–F · 1984 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1975 Å² buried · 10 hydrogen bonds · protein-protein
L–H · 1959 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1932 Å² buried · 14 hydrogen bonds · protein-protein
H–D · 1272 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

3CFJ · Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal form · 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
Every structure of UniProt Q8TCD0
Every structure of UniProt A8K008
Elsewhere: RCSB PDB 3CFJ · PDBe 3CFJ · UniProt Q8TCD0 · UniProt A8K008

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