MolNFT v1 · #153896 · protein

Mouse antibody 3.3 Fab in complex with peg

6JU0 · Fab heavy chain: “Mouse antibody 3.3 Fab in complex with peg”. X-ray diffraction, 1 ligand (TOE), 17 pockets (best druggability 0.67). MolNFT v1 #153896 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JU0
Type: protein
Length: 1,702 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain
Ligands: TOE
Pockets: 17 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, J	Fab heavy chain	protein	212	8% helix, 55% strand	—
L, M, N, O	Fab light chain	protein	213	8% helix, 51% strand	—
I, K	Fab heavy chain	protein	213	8% helix, 54% strand	—

Ligands and binding sites

TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 4 copies · chains H, L, I, M, J, N, K, O
PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 2 copies · chains H, L, I, M, J, N, K, O
1PE · Pentaethylene glycol · additive · chains H
PG4 · Tetraethylene glycol · additive · chains K

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	466	0.67	0.79	50	empty
2	743	0.66	0.75	73	empty
3	436	0.65	0.78	44	empty
4	669	0.65	0.75	62	empty
5	720	0.65	0.74	75	empty

Interfaces

14 interfaces between chains.

H–L · 1792 Å² buried · 17 hydrogen bonds · protein-protein
K–O · 1789 Å² buried · 15 hydrogen bonds · protein-protein
J–N · 1781 Å² buried · 15 hydrogen bonds · protein-protein
I–M · 1760 Å² buried · 16 hydrogen bonds · protein-protein
I–K · 411 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 modified (disulfide, cyclization).

Compared structures

6JU0 · Mouse antibody 3.3 Fab in complex with PEG · the same entry in another collection · chain H against H, 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 6JU0 · PDBe 6JU0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.