MolNFT v1 · #139663 · protein
Crystal structure of an IgM rheumatoid factor YES8C in complex with IGG1 Fc
5XMH · Immunoglobulin gamma-1 heavy chain: “Crystal structure of an IgM rheumatoid factor YES8C in complex with IGG1 Fc”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.63). MolNFT v1 #139663 on GenesisL1: 3D…
- 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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