MolNFT v1 · #163512 · protein
Crystal structure of Fc P329G lala with anti Fc P329G Fab
6S5A: “Crystal structure of Fc P329G lala with anti Fc P329G Fab”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 9 pockets (best druggability 0.66). MolNFT v1 #163512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S5A
- Type
- protein
- Length
- 855 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fc P329G lala; Anti P329G lala Fab heavy chain; Anti P329G lala Fab light chain
- Ligands
- NAG, MAN, BMA, FUC, PO4
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fc P329G lala | protein | 213 | 10% helix, 47% strand | — |
| D | Fc P329G lala | protein | 209 | 11% helix, 48% strand | — |
| H | Anti P329G lala Fab heavy chain | protein | 221 | 11% helix, 50% strand | — |
| L | Anti P329G lala Fab light chain | protein | 212 | 8% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, D, L, H
- GOL · Glycerol · additive · 3 copies · chains D, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.66 | 0.75 | 63 | PO4 |
| 2 | 563 | 0.61 | 0.74 | 67 | empty |
| 3 | 152 | 0.46 | 0.76 | 25 | empty |
| 4 | 96 | 0.43 | 0.78 | 25 | PO4 |
| 5 | 116 | 0.42 | 0.76 | 24 | GOL |
Interfaces
6 interfaces between chains.
- H–L · 1753 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1235 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 483 Ų buried · 8 hydrogen bonds · protein-protein
- D–L · 424 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 171 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6S5A · Crystal structure of Fc P329G lala with anti Fc P329G Fab · 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
- Elsewhere: RCSB PDB 6S5A · PDBe 6S5A
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