MolNFT v1 · #65449 · protein

Crystal structure of vwf A2 domain

3GXB · Von willebrand factor: “Crystal structure of vwf A2 domain”. X-ray diffraction, 2 ligands (NAG, SO4), 2 pockets (best druggability 0.54). MolNFT v1 #65449 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3GXB
Type: protein
Length: 354 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Von willebrand factor
UniProt: P04275
Ligands: NAG, SO4
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Von willebrand factor	protein	177	36% helix, 23% strand	P04275

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
SO4 · Sulfate ion · ion · chains B

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

Pockets

2 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	254	0.54	0.76	21	empty
2	156	0.45	0.76	34	empty

Interfaces

1 interface between chains.

A–B · 203 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

3GXB · Crystal structure of VWF A2 domain · 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 3GXB · PDBe 3GXB · UniProt P04275

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