MolNFT v1 · #154955 · protein
Crystal structure of mouse IGG2B Fc complexed with B domain of protein a
6KRV · Ig gamma-2B chain C region: “Crystal structure of mouse IGG2B Fc complexed with B domain of protein a”. X-ray diffraction, 3 ligands (NAG, MAN, FUC), 6 pockets (best druggability 0.41). MolNFT v1 #154955 on GenesisL1: 3D structure…
- PDB
- 6KRV
- Type
- protein
- Length
- 621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-2B chain C region; Immunoglobulin G-binding protein a
- UniProt
- P01867, P38507
- Ligands
- NAG, MAN, FUC
- Pockets
- 6 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-2B chain C region | protein | 207 | 10% helix, 50% strand | P01867 |
| B | Ig gamma-2B chain C region | protein | 154 | 15% helix, 33% strand | P01867 |
| C | Ig gamma-2B chain C region | protein | 208 | 11% helix, 50% strand | P01867 |
| D | Immunoglobulin G-binding protein a | protein | 52 | 79% helix, 0% strand | P38507 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.41 | 0.78 | 18 | empty |
| 2 | 54 | 0.39 | 0.80 | 14 | empty |
| 3 | 104 | 0.38 | 0.76 | 19 | empty |
| 4 | 58 | 0.29 | 0.74 | 15 | empty |
| 5 | 56 | 0.26 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1129 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 984 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 743 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6KRV · Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A · the same entry in another collection · chain A against A, TM-score 1.00
- P01867 · AlphaFold monomer V2.0 prediction for ig gamma-2B chain C region (P01867) · a predicted model of the same protein · chain C against A, TM-score 0.98
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
- Every structure of UniProt P38507
- Elsewhere: RCSB PDB 6KRV · PDBe 6KRV · UniProt P01867 · UniProt P38507
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