MolNFT v1 · #135869 · protein
Crystal structure of a mutant MIGG2B Fc heterodimer in complex with protein a peptide analog Z34C
5UBX · Ig gamma-2B chain C region: “Crystal structure of a mutant MIGG2B Fc heterodimer in complex with protein a peptide analog Z34C”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.34). MolNFT v1 #135869 on…
- PDB
- 5UBX
- Type
- protein
- Length
- 426 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-2B chain C region; Peptide analog of B-domain from protein a - Z34C
- UniProt
- P01867
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-2B chain C region | protein | 191 | 12% helix, 46% strand | P01867 |
| B | Ig gamma-2B chain C region | protein | 201 | 11% helix, 50% strand | P01867 |
| Z | Peptide analog of B-domain from protein a - Z34C | protein | 34 | 74% helix, 0% 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
- FUC · alpha-L-fucopyranose · sugar · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.34 | 0.76 | 17 | empty |
| 2 | 63 | 0.34 | 0.76 | 18 | empty |
| 3 | 55 | 0.27 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1115 Ų buried · 12 hydrogen bonds · protein-protein
- A–Z · 740 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5UBX · Crystal structure of a mutant mIgG2b Fc heterodimer in complex with Protein A peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P01867 · AlphaFold monomer V2.0 prediction for ig gamma-2B chain C region (P01867) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01867
- Elsewhere: RCSB PDB 5UBX · PDBe 5UBX · UniProt P01867
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