MolNFT v1 · #148777 · protein
Fc in complex with engineered calcium binding domain Z
6FGO · Immunoglobulin gamma-1 heavy chain: “Fc in complex with engineered calcium binding domain Z”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.67). MolNFT v1 #148777 on GenesisL1: 3D structure, binding…
- PDB
- 6FGO
- Type
- protein
- Length
- 1,094 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain; Z-ca
- UniProt
- P0DOX5
- Ligands
- NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin gamma-1 heavy chain | protein | 209 | 11% helix, 48% strand | P0DOX5 |
| E | Z-ca | protein | 64 | 59% helix, 0% strand | — |
| F | Z-ca | protein | 67 | 57% helix, 0% strand | — |
| C, D | Immunoglobulin gamma-1 heavy chain | protein | 208 | 11% helix, 48% strand | P0DOX5 |
| G | Z-ca | protein | 65 | 58% helix, 0% strand | — |
| H | Z-ca | protein | 64 | 59% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, F, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, F, C
- CA · Calcium ion · metal · 4 copies · chains E, F, G, H
- CL · Chloride ion · ion · 9 copies · chains B, C, F, D
- GOL · Glycerol · additive · 15 copies · chains A, C, E, B, F, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.67 | 0.78 | 64 | GOL |
| 2 | 218 | 0.47 | 0.74 | 34 | empty |
| 3 | 118 | 0.42 | 0.77 | 27 | empty |
| 4 | 106 | 0.42 | 0.77 | 16 | empty |
| 5 | 92 | 0.40 | 0.77 | 17 | CL |
Interfaces
10 interfaces between chains.
- A–C · 1135 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1126 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 839 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 769 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 756 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6FGO · Fc in complex with engineered calcium binding domain Z · 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 6FGO · PDBe 6FGO · UniProt P0DOX5
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