MolNFT v1 · #168422 · protein

Fab portion of dupilumab with crystal kappa design

6WG8 · Dupilumab Fab heavy chain: “Fab portion of dupilumab with crystal kappa design”. X-ray diffraction, 6 pockets (best druggability 0.67). MolNFT v1 #168422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WG8
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dupilumab Fab heavy chain; Dupilumab Fab light chain
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dupilumab Fab heavy chain	protein	218	7% helix, 51% strand	—
B	Dupilumab Fab light chain	protein	216	6% helix, 54% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	752	0.67	0.75	63	GOL
2	58	0.48	0.86	25	GOL
3	81	0.37	0.77	19	empty
4	91	0.32	0.73	28	empty
5	56	0.28	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1849 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6WG8 · Fab portion of dupilumab with Crystal Kappa design · the same entry in another collection · chain A against A, 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 6WG8 · PDBe 6WG8

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