MolNFT v1 · #59727 · protein
Crystal structure of Fab F22-4 in complex with a shigella flexneri 2A O-ag pentadecasaccharide
3C6S · Fab F22-4 light chain: “Crystal structure of Fab F22-4 in complex with a shigella flexneri 2A O-ag pentadecasaccharide”. X-ray diffraction, 4 ligands (RAM, NAG, GLC), 20 pockets (best druggability 0.81). MolNFT v1 #59727 on…
- PDB
- 3C6S
- Type
- protein
- Length
- 1,702 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab F22-4 light chain; Fab F22-4 heavy chain
- Ligands
- RAM, NAG, GLC, PD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Fab F22-4 light chain | protein | 216 | 6% helix, 50% strand | — |
| B, D, F, H | Fab F22-4 heavy chain | protein | 209 | 11% helix, 54% strand | — |
| C | Fab F22-4 light chain | protein | 218 | 6% helix, 49% strand | — |
Ligands and binding sites
- RAM · alpha-L-rhamnopyranose · sugar · 28 copies · chains A, B, C, D, E, F, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains B, A, D, C, F, E, H, G
- PD · Palladium ion · metal · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.81 | 0.83 | 117 | empty |
| 2 | 690 | 0.64 | 0.74 | 80 | empty |
| 3 | 416 | 0.62 | 0.77 | 38 | empty |
| 4 | 386 | 0.57 | 0.75 | 33 | empty |
| 5 | 333 | 0.57 | 0.76 | 47 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1676 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1675 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1617 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1602 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 395 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3C6S · Crystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag… · 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 3C6S · PDBe 3C6S
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.