MolNFT v1 · #40563 · protein
Complex between the pryspry domain of TRIM21 and IgG Fc
2IWG · Ig gamma-1 chain C: “Complex between the pryspry domain of TRIM21 and IgG Fc”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.70). MolNFT v1 #40563 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2IWG
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C; 52 kda ro protein
- UniProt
- P01857, P19474
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ig gamma-1 chain C | protein | 207 | 11% helix, 49% strand | P01857 |
| B, E | 52 kda ro protein | protein | 181 | 0% helix, 38% strand | P19474 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.70 | 0.87 | 30 | empty |
| 2 | 247 | 0.70 | 0.85 | 36 | empty |
| 3 | 232 | 0.65 | 0.83 | 35 | empty |
| 4 | 309 | 0.65 | 0.81 | 55 | empty |
| 5 | 180 | 0.54 | 0.79 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1149 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 804 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 802 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2IWG · Complex between the pryspry domain of TRIM21 and IgG Fc · the same entry in another collection · chain A against A, TM-score 1.00
- P19474 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM21 (P19474) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P19474
- Elsewhere: RCSB PDB 2IWG · PDBe 2IWG · UniProt P01857 · UniProt P19474
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