MolNFT v1 · #17354 · protein
G-2 glycovariant of human IgG Fc bound to minimized version of protein a called Z34C
1OQX · Immunoglobulin gamma-1 heavy chain constant region: “G-2 glycovariant of human IgG Fc bound to minimized version of protein a called Z34C”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 2 pockets (best druggability 0.35). MolNFT v1…
- PDB
- 1OQX
- Type
- protein
- Length
- 487 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain constant region; Protein a Z34C
- Ligands
- NAG, BMA, MAN, FUL, FUC
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain constant region | protein | 210 | 10% helix, 46% strand | — |
| B | Immunoglobulin gamma-1 heavy chain constant region | protein | 209 | 10% helix, 50% strand | — |
| C, D | Protein a Z34C | protein | 34 | 74% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.35 | 0.73 | 24 | empty |
| 2 | 61 | 0.29 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1149 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 753 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 717 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1OQX · G-2 glycovariant of human IgG Fc bound to minimized version of Protein A called Z34C · the same entry in another collection · chain B against B, 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 1OQX · PDBe 1OQX
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