MolNFT v1 · #76594 · protein

Crystal structure of anti-TLR3 antibody C1068 Fab

3QPQ · C1068 light chain: “Crystal structure of anti-TLR3 antibody C1068 Fab”. X-ray diffraction, 1 ligand (SO4), 18 pockets (best druggability 0.66). MolNFT v1 #76594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QPQ
Type: protein
Length: 1,733 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C1068 light chain; C1068 heavy chain
Ligands: SO4
Pockets: 18 · best druggability 0.66

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, E, C, I	C1068 light chain	protein	215	6% helix, 50% strand	—
H	C1068 heavy chain	protein	216	11% helix, 50% strand	—
F	C1068 heavy chain	protein	221	10% helix, 49% strand	—
D	C1068 heavy chain	protein	219	10% helix, 49% strand	—
J	C1068 heavy chain	protein	217	10% helix, 49% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains L, H
GOL · Glycerol · additive · 17 copies · chains L, H, E, F, C, D, I, J

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

Pockets

18 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	707	0.66	0.74	67	empty
2	477	0.61	0.75	57	empty
3	464	0.61	0.75	51	empty
4	221	0.60	0.81	42	empty
5	385	0.56	0.74	45	GOL

Interfaces

10 interfaces between chains.

C–D · 1996 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 1902 Å² buried · 16 hydrogen bonds · protein-protein
L–H · 1861 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1822 Å² buried · 14 hydrogen bonds · protein-protein
H–C · 348 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 4 modified (disulfide, cyclization).

Compared structures

3QPQ · Crystal structure of ANTI-TLR3 antibody C1068 FAB · 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 3QPQ · PDBe 3QPQ

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