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2 helix minimized version of the B-domain from protein a (Z34C0 bound to IGG1 Fc (monoclinic form)
Analyse 2 helix minimized version of the B-domain from protein a (Z34C0 bound to IGG1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U52
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 Fc; Mini Z domain
- UniProt
- Q6MZV7
- Ligands
- NAG, MAN, GAL, FUC
- Pockets
- 4 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG1 Fc | protein | 207 | 11% helix, 48% strand | Q6MZV7 |
| B | IGG1 Fc | protein | 209 | 11% helix, 47% strand | Q6MZV7 |
| E, Z | Mini Z domain | protein | 34 | 74% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.36 | 0.76 | 19 | empty |
| 2 | 62 | 0.33 | 0.77 | 17 | empty |
| 3 | 62 | 0.31 | 0.75 | 19 | empty |
| 4 | 73 | 0.30 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1164 Ų buried · 8 hydrogen bonds · protein-protein
- B–Z · 775 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 731 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5U52 · 2 helix minimized version of the B-domain from Protein A (Z34C0 bound to IgG1 Fc… · 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 Q6MZV7
- Elsewhere: RCSB PDB 5U52 · PDBe 5U52 · UniProt Q6MZV7
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