MolNFT v1 · #40875 · protein
Crystal structure of an autoimmune complex between a human IgM rheumatoid factor and IGG1 Fc reveals a novel Fc epitope and evidence for affinity maturation
2J6E · Ig gamma-1 chain C region: “Crystal structure of an autoimmune complex between a human IgM rheumatoid factor and IGG1 Fc reveals a novel…”. X-ray diffraction, 7 ligands (NAG, BMA, MAN), 10 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 2J6E
- Type
- protein
- Length
- 1,281 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; IgM
- UniProt
- P01857
- Ligands
- NAG, BMA, MAN, GAL, FUL, ZN, CD
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 209 | 11% helix, 50% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 208 | 11% helix, 42% strand | P01857 |
| H | IgM | protein | 216 | 3% helix, 41% strand | — |
| I | IgM | protein | 220 | 5% helix, 45% strand | — |
| L | IgM | protein | 213 | 3% helix, 37% strand | — |
| M | IgM | protein | 215 | 4% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CD · Cadmium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, I, M
- ACT · Acetate ion · additive · 4 copies · chains A, B, I, H
- CAC · Cacodylate ion · additive · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.78 | 0.82 | 55 | empty |
| 2 | 458 | 0.58 | 0.74 | 53 | MPD |
| 3 | 143 | 0.55 | 0.81 | 23 | ACT |
| 4 | 141 | 0.52 | 0.80 | 19 | empty |
| 5 | 138 | 0.51 | 0.80 | 25 | empty |
Interfaces
10 interfaces between chains.
- I–M · 1834 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1718 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1157 Ų buried · 8 hydrogen bonds · protein-protein
- B–I · 436 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 427 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2J6E · Crystal Structure of an Autoimmune Complex between a Human IgM Rheumatoid Factor and IgG1… · 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
- Elsewhere: RCSB PDB 2J6E · PDBe 2J6E · UniProt P01857
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