Research workbench
Crystal structure of high-affinity von willebrand factor A1 domain with R1306Q and I1309V mutations in complex with high affinity gpib alpha
Analyse Crystal structure of high-affinity von willebrand factor A1 domain with R1306Q… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C2A
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand factor; Platelet glycoprotein ib alpha chain
- UniProt
- P04275, P07359
- Ligands
- CA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Von willebrand factor | protein | 202 | 39% helix, 22% strand | P04275 |
| B | Platelet glycoprotein ib alpha chain | protein | 266 | 9% helix, 21% strand | P07359 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- CAC · Cacodylate ion · additive · chains A
- ACT · Acetate ion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.79 | 0.81 | 72 | PEG |
| 2 | 89 | 0.42 | 0.79 | 18 | empty |
| 3 | 139 | 0.40 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1186 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4C2A · Crystal Structure of High-Affinity von Willebrand Factor A1 domain with R1306Q and I1309V… · the same entry in another collection · chain A against A, TM-score 1.00
- P07359 · AlphaFold monomer V2.0 prediction for platelet glycoprotein ib alpha chain (P07359) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P07359
- Elsewhere: RCSB PDB 4C2A · PDBe 4C2A · UniProt P04275 · UniProt P07359
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