MolNFT v1 · #37998 · protein
Crystal structure of a ge-GI/FC complex
2GJ7 · Ig gamma-1 chain C region: “Crystal structure of a ge-GI/FC complex”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.44). MolNFT v1 #37998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GJ7
- Type
- protein
- Length
- 756 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; Glycoprotein E
- UniProt
- P01857, P04488
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 5 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ig gamma-1 chain C region | protein | 207 | 11% helix, 49% strand | P01857 |
| F, E | Glycoprotein E | protein | 171 | 9% helix, 45% strand | P04488 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.44 | 0.77 | 22 | empty |
| 2 | 135 | 0.43 | 0.76 | 24 | empty |
| 3 | 83 | 0.34 | 0.75 | 23 | empty |
| 4 | 61 | 0.31 | 0.76 | 21 | empty |
| 5 | 50 | 0.26 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1168 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 1035 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 926 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2GJ7 · Crystal Structure of a gE-gI/Fc complex · 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 P01857
- Every structure of UniProt P04488
- Elsewhere: RCSB PDB 2GJ7 · PDBe 2GJ7 · UniProt P01857 · UniProt P04488
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