MolNFT v1 · #154954 · protein
Crystal structure of mouse IGG2B Fc
6KRU · Ig gamma-2B chain C region: “Crystal structure of mouse IGG2B Fc”. X-ray diffraction, 4 ligands (NAG, MAN, GAL), 13 pockets (best druggability 0.78). MolNFT v1 #154954 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KRU
- Type
- protein
- Length
- 1,215 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-2B chain C region
- UniProt
- P01867
- Ligands
- NAG, MAN, GAL, FUC
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ig gamma-2B chain C region | protein | 208 | 11% helix, 49% strand | P01867 |
| C | Ig gamma-2B chain C region | protein | 203 | 11% helix, 51% strand | P01867 |
| D | Ig gamma-2B chain C region | protein | 201 | 11% helix, 50% strand | P01867 |
| E | Ig gamma-2B chain C region | protein | 191 | 12% helix, 49% strand | P01867 |
| F | Ig gamma-2B chain C region | protein | 204 | 12% helix, 50% strand | P01867 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, D, B, C, E, F
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains A, D, B, C, E, F
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.78 | 0.82 | 86 | empty |
| 2 | 679 | 0.76 | 0.82 | 72 | empty |
| 3 | 127 | 0.45 | 0.78 | 20 | empty |
| 4 | 129 | 0.44 | 0.77 | 23 | empty |
| 5 | 110 | 0.40 | 0.77 | 21 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1142 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1140 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1081 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 335 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 304 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 P01867
- Elsewhere: RCSB PDB 6KRU · PDBe 6KRU · UniProt P01867
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