Research workbench
Complex between G0 version of an Fc bound to a minimized version of protein a called mini-Z
Analyse Complex between G0 version of an Fc bound to a minimized version of protein a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OQO
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain constant region; Minimized version of protein a (Z34C)
- Ligands
- NAG, MAN, BMA, FUL, NDG, FUC
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain constant region | protein | 208 | 10% helix, 48% strand | — |
| C, D | Minimized version of protein a (Z34C) | protein | 34 | 74% helix, 0% strand | — |
| B | Immunoglobulin gamma-1 heavy chain constant region | protein | 208 | 10% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.28 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1157 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 739 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 726 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1OQO · Complex between G0 version of an Fc bound to a minimized version of Protein A called… · 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
- Elsewhere: RCSB PDB 1OQO · PDBe 1OQO
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