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Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)
Analyse Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VN4
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A disintegrin and metalloproteinase with thrombospondin motifs 13
- EC
- 3.4.24.87
- UniProt
- Q76LX8
- Ligands
- NAG, FUC, BGC, BMA
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A disintegrin and metalloproteinase with thrombospondin motifs 13 (EC 3.4.24.87) | protein | 375 | 10% helix, 32% strand | Q76LX8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.66 | 0.80 | 48 | empty |
| 2 | 79 | 0.35 | 0.76 | 24 | empty |
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation, C-mannosylation, O-glycosylation).
Compared structures
- 3VN4 · Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant) · the same entry in another collection · chain A against A, TM-score 1.00
- Q76LX8 · AlphaFold monomer V2.0 prediction for a disintegrin and metalloproteinase with… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q76LX8
- Elsewhere: RCSB PDB 3VN4 · PDBe 3VN4 · UniProt Q76LX8
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