MolNFT v1 · #146004 · protein
Crystal structure of a Fc fragment of rhesus macaque (macaca mulatta) IGG3
6D4M · Fc fragment of IGG3: “Crystal structure of a Fc fragment of rhesus macaque (macaca mulatta) IGG3”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.40). MolNFT v1 #146004 on GenesisL1: 3D structure…
- PDB
- 6D4M
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fc fragment of IGG3
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fc fragment of IGG3 | protein | 208 | 6% helix, 34% strand | — |
| B | Fc fragment of IGG3 | protein | 209 | 4% helix, 44% strand | — |
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
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 | 101 | 0.40 | 0.77 | 17 | empty |
| 2 | 51 | 0.39 | 0.81 | 11 | empty |
| 3 | 77 | 0.34 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1162 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6D4M · Crystal Structure of a Fc Fragment of Rhesus macaque (Macaca mulatta) IgG3 · 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 6D4M · PDBe 6D4M
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