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Crystal structure of the von willebrand factor A3 domain in complex with a collagen III derived triple-helical peptide

Analyse Crystal structure of the von willebrand factor A3 domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DMU
Type: protein
Length: 1,605 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collagen III derived triple-helical peptide; Von willebrand factor
UniProt: P04275
Ligands: SO4
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I	Collagen III derived triple-helical peptide	protein	79	0% helix, 0% strand	—
B, D, F, L	Von willebrand factor	protein	188	39% helix, 21% strand	P04275
H	Von willebrand factor	protein	187	40% helix, 22% strand	P04275
J	Von willebrand factor	protein	191	36% helix, 21% strand	P04275
K	Collagen III derived triple-helical peptide	protein	80	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains C, D, E, F, I, J, K, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	938	0.81	0.82	76	SO4
2	918	0.76	0.79	84	SO4
3	517	0.69	0.79	59	empty
4	449	0.66	0.78	52	empty
5	272	0.64	0.81	50	empty

Interfaces

23 interfaces between chains.

G–H · 790 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 770 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 754 Å² buried · 5 hydrogen bonds · protein-protein
I–J · 748 Å² buried · 6 hydrogen bonds · protein-protein
K–L · 740 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 126 modified, 5 disulfide (hydroxylation, disulfide).

Compared structures

4DMU · Crystal structure of the von Willebrand factor A3 domain in complex with a collagen III… · 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
Every structure of UniProt P04275
Elsewhere: RCSB PDB 4DMU · PDBe 4DMU · UniProt P04275

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