Research workbench
Crystal structure of an IgM rheumatoid factor YES8C in complex with IGG1 Fc
Analyse Crystal structure of an IgM rheumatoid factor YES8C in complex with IGG1 Fc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XMH
- Type
- protein
- Length
- 1,076 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain; YES8C light chain; YES8C heavy chain
- UniProt
- P0DOX5
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain | protein | 208 | 11% helix, 49% strand | P0DOX5 |
| B | Immunoglobulin gamma-1 heavy chain | protein | 207 | 10% helix, 49% strand | P0DOX5 |
| L | YES8C light chain | protein | 214 | 7% helix, 53% strand | — |
| H | YES8C heavy chain | protein | 217 | 4% helix, 48% strand | — |
| D | YES8C heavy chain | protein | 123 | 5% helix, 47% strand | — |
| C | YES8C light chain | protein | 107 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.63 | 0.76 | 55 | empty |
| 2 | 289 | 0.59 | 0.78 | 27 | empty |
| 3 | 324 | 0.53 | 0.74 | 45 | empty |
| 4 | 56 | 0.31 | 0.75 | 18 | empty |
| 5 | 55 | 0.30 | 0.77 | 20 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1582 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 5 hydrogen bonds · protein-protein
- D–C · 684 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 672 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 639 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5XMH · Crystal structure of an IgM rheumatoid factor YES8c in complex with IgG1 Fc · 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 P0DOX5
- Elsewhere: RCSB PDB 5XMH · PDBe 5XMH · UniProt P0DOX5
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