MolNFT v1 · #116843 · protein
Structure of S55-5 Fab in complex with lipid a carbohydrate backbone
5DQD · S55-5 Fab (IGG1 kappa) light chain: “Structure of S55-5 Fab in complex with lipid a carbohydrate backbone”. X-ray diffraction, 3 ligands (GN1, GN4, CL), 5 pockets (best druggability 0.68). MolNFT v1 #116843 on GenesisL1: 3D…
- PDB
- 5DQD
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S55-5 Fab (IGG1 kappa) light chain; S55-5 Fab (IGG1) heavy chain
- Ligands
- GN1, GN4, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | S55-5 Fab (IGG1 kappa) light chain | protein | 217 | 6% helix, 53% strand | — |
| H | S55-5 Fab (IGG1) heavy chain | protein | 222 | 7% helix, 50% strand | — |
Ligands and binding sites
- GN1 · 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · chains H
- GN4 · 2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · chains L, H
- CL · Chloride ion · ion · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.68 | 0.76 | 71 | empty |
| 2 | 257 | 0.56 | 0.77 | 37 | empty |
| 3 | 109 | 0.42 | 0.77 | 19 | GN4 |
| 4 | 77 | 0.34 | 0.75 | 17 | CL |
| 5 | 51 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- L–H · 2138 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5DQD · Structure of S55-5 Fab in complex with lipid A carbohydrate backbone · the same entry in another collection · chain H against H, 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 5DQD · PDBe 5DQD
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