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Crystal structure and paratope determination of 82D6A3, an antithrombotic antibody directed against the von willebrand factor A3-domain

Analyse Crystal structure and paratope determination of 82D6A3, an antithrombotic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ADF
Type: protein
Length: 616 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Von willebrand factor; 82D6A3 IgG
UniProt: P04275, P84751, Q58EV6
Ligands: SO4
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Von willebrand factor	protein	189	42% helix, 22% strand	P04275
H	82D6A3 IgG	protein	218	8% helix, 53% strand	P84751
L	82D6A3 IgG	protein	209	6% helix, 51% strand	Q58EV6

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains H, L
ACY · Acetic acid · additive · chains A
GOL · Glycerol · additive · chains H, L

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	394	0.56	0.74	47	GOL
2	87	0.56	0.86	31	empty
3	228	0.50	0.75	35	empty
4	116	0.44	0.77	23	empty
5	86	0.38	0.77	25	empty

Interfaces

3 interfaces between chains.

H–L · 1909 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 637 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 325 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2ADF · Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody… · the same entry in another collection · chain L against L, TM-score 1.00
P84751 · AlphaFold monomer V2.0 prediction for ig heavy chain MEM5 (P84751) · a predicted model of the same protein · chain H against A, TM-score 0.87

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 P04275
Every structure of UniProt P84751
Every structure of UniProt Q58EV6
Elsewhere: RCSB PDB 2ADF · PDBe 2ADF · UniProt P04275 · UniProt P84751 · UniProt Q58EV6

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