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Crystal structure of a motavizumab epitope-scaffold bound to motavizumab Fab

Analyse Crystal structure of a motavizumab epitope-scaffold bound to motavizumab Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QWO
Type: protein
Length: 966 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Motavizumab light chain; Motavizumab heavy chain; Motavizumab epitope scaffold
Ligands: SO4
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, B	Motavizumab light chain	protein	210	6% helix, 55% strand	—
H, A	Motavizumab heavy chain	protein	220	8% helix, 51% strand	—
C, P	Motavizumab epitope scaffold	protein	53	83% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains L, H, B
EDO · 1,2-ethanediol · additive · 3 copies · chains H, B, A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1001	0.75	0.78	124	empty
2	1050	0.75	0.78	109	EDO
3	56	0.51	0.88	20	empty
4	62	0.35	0.78	17	empty
5	64	0.28	0.73	17	empty

Interfaces

11 interfaces between chains.

L–H · 1864 Å² buried · 15 hydrogen bonds · protein-protein
B–A · 1836 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 556 Å² buried · 6 hydrogen bonds · protein-protein
H–P · 520 Å² buried · 6 hydrogen bonds · protein-protein
L–P · 294 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3QWO · Crystal structure of a motavizumab epitope-scaffold bound to motavizumab 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 3QWO · PDBe 3QWO

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