MolNFT v1 · #137181 · protein
Fc fragment of human IGG1 antibody, from nist mab
5VGP · Human Fc fragment with G1F/G0F glycan: “Fc fragment of human IGG1 antibody, from nist mab”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.31). MolNFT v1 #137181 on GenesisL1: 3D structure, binding…
- PDB
- 5VGP
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human Fc fragment with G1F/G0F glycan
- UniProt
- Q6PYX1
- Ligands
- NAG, MAN, BMA, FUC, GAL
- Pockets
- 3 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Human Fc fragment with G1F/G0F glycan | protein | 209 | 10% helix, 47% strand | Q6PYX1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 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 · 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
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 | 67 | 0.31 | 0.75 | 15 | empty |
| 2 | 71 | 0.30 | 0.73 | 18 | empty |
| 3 | 52 | 0.23 | 0.71 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1202 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VGP · Fc fragment of human IgG1 antibody, from NIST mAb · 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 Q6PYX1
- Elsewhere: RCSB PDB 5VGP · PDBe 5VGP · UniProt Q6PYX1
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