MolNFT v1 · #135638 · protein
IgG Fc bound to 3 helix of the B-domain from protein a
5U4Y · IGG1 Fc: “IgG Fc bound to 3 helix of the B-domain from protein a”. X-ray diffraction, 4 ligands (NAG, MAN, FUC), 4 pockets (best druggability 0.38). MolNFT v1 #135638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U4Y
- Type
- protein
- Length
- 527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 Fc; Immunoglobulin G-binding protein a
- UniProt
- Q6MZV7
- Ligands
- NAG, MAN, FUC, GAL
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG1 Fc | protein | 207 | 11% helix, 48% strand | Q6MZV7 |
| B | IGG1 Fc | protein | 212 | 11% helix, 47% strand | Q6MZV7 |
| C | Immunoglobulin G-binding protein a | protein | 53 | 79% helix, 0% strand | — |
| D | Immunoglobulin G-binding protein a | protein | 55 | 76% 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
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 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 | 140 | 0.38 | 0.73 | 27 | empty |
| 2 | 71 | 0.31 | 0.75 | 17 | empty |
| 3 | 61 | 0.29 | 0.74 | 16 | empty |
| 4 | 58 | 0.26 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1260 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 858 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 731 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5U4Y · IgG Fc bound to 3 helix of the B-domain from Protein A · 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 5U4Y · PDBe 5U4Y · UniProt Q6MZV7
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