Research workbench
Crystal structure of the von willebrand factor A3 domain in complex with a Fab fragment of IgG RU5 that inhibits collagen binding
Analyse Crystal structure of the von willebrand factor A3 domain in complex with a Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FE8
- Type
- protein
- Length
- 1,834 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand factor; Immunoglobulin IgG RU5
- UniProt
- P04275
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Von willebrand factor | protein | 190 | 37% helix, 21% strand | P04275 |
| H, I, J | Immunoglobulin IgG RU5 | protein | 210 | 7% helix, 52% strand | — |
| L, M, N | Immunoglobulin IgG RU5 | protein | 211 | 6% helix, 51% strand | — |
| C | Von willebrand factor | protein | 191 | 38% helix, 21% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains H, I, J
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, H, B, I, C, J
- CAC · Cacodylate ion · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.73 | 0.84 | 57 | empty |
| 2 | 1032 | 0.73 | 0.77 | 107 | empty |
| 3 | 334 | 0.71 | 0.84 | 51 | empty |
| 4 | 692 | 0.68 | 0.76 | 61 | empty |
| 5 | 176 | 0.61 | 0.83 | 39 | empty |
Interfaces
19 interfaces between chains.
- J–N · 1813 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1812 Ų buried · 14 hydrogen bonds · protein-protein
- I–M · 1765 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 975 Ų buried · 22 hydrogen bonds · protein-protein
- C–N · 592 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 12 modified, 3 glycan (disulfide, engineered, N-glycosylation).
Compared structures
- 1FE8 · Crystal structure of the von willebrand factor A3 domain in complex with a Fab fragment… · 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 1FE8 · PDBe 1FE8 · UniProt P04275
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