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

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

PDB: 3CFK
Type: protein
Length: 3,512 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic antibody Fab 34E4 light CHAIN,UNCHARACTERIZED protein; Catalytic antibody Fab…
UniProt: Q8TCD0, A8K008
Ligands: CD
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A, C, E, G, J, M, O	Catalytic antibody Fab 34E4 light CHAIN,UNCHARACTERIZED protein	protein	215	7% helix, 53% strand	Q8TCD0
H, B, D, F, I, K, N, P	Catalytic antibody Fab 34E4 heavy CHAIN,UNCHARACTERIZED protein	protein	224	11% helix, 53% strand	A8K008

Ligands and binding sites

CD · Cadmium ion · metal · 23 copies · chains L, J, H, K, A, M, B, C, G, D, P, E, O, F, I
GOL · Glycerol · additive · 2 copies · chains A, M, E, O
B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains M, O

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.83	0.84	126	empty
2	1051	0.82	0.83	136	empty
3	956	0.81	0.83	137	empty
4	816	0.80	0.83	107	empty
5	747	0.79	0.83	93	CD

Interfaces

42 interfaces between chains.

C–D · 2021 Å² buried · 14 hydrogen bonds · protein-protein
O–P · 1983 Å² buried · 12 hydrogen bonds · protein-protein
J–K · 1982 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1980 Å² buried · 13 hydrogen bonds · protein-protein
G–I · 1972 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide, 1 covalent (disulfide, additive adduct).

Compared structures

3CFK · Crystal structure of catalytic elimination antibody 34E4, triclinic 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 3CFK · PDBe 3CFK · UniProt Q8TCD0 · UniProt A8K008

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