MolNFT v1 · #137365 · protein
Crystal structure of human IGG1 Fc K248E, T437R mutant
5VME · Human IGG1 Fc K248E,T437R mutant: “Crystal structure of human IGG1 Fc K248E, T437R mutant”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.42). MolNFT v1 #137365 on GenesisL1: 3D structure, binding…
- PDB
- 5VME
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human IGG1 Fc K248E,T437R mutant
- UniProt
- Q6MZV7
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human IGG1 Fc K248E,T437R mutant | protein | 207 | 12% helix, 48% strand | Q6MZV7 |
| B | Human IGG1 Fc K248E,T437R mutant | protein | 196 | 10% helix, 50% strand | Q6MZV7 |
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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.42 | 0.83 | 12 | empty |
| 2 | 62 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1111 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VME · Crystal structure of human IgG1 Fc K248E, T437R mutant · 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 Q6MZV7
- Elsewhere: RCSB PDB 5VME · PDBe 5VME · UniProt Q6MZV7
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