MolNFT v1 · #116839 · protein
Structure of S55-3 Fab in complex with lipid a
5DQ9 · S55-3 Fab (IGG2B) heavy chain: “Structure of S55-3 Fab in complex with lipid a”. X-ray diffraction, 3 ligands (GN1, GN4, CL), 12 pockets (best druggability 0.74). MolNFT v1 #116839 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DQ9
- Type
- protein
- Length
- 1,292 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S55-3 Fab (IGG2B) heavy chain; Mab 44B1 light chain
- Ligands
- GN1, GN4, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S55-3 Fab (IGG2B) heavy chain | protein | 218 | 6% helix, 52% strand | — |
| B | Mab 44B1 light chain | protein | 212 | 7% helix, 54% strand | — |
| C | S55-3 Fab (IGG2B) heavy chain | protein | 217 | 6% helix, 52% strand | — |
| D | Mab 44B1 light chain | protein | 211 | 7% helix, 55% strand | — |
| H | S55-3 Fab (IGG2B) heavy chain | protein | 222 | 5% helix, 51% strand | — |
| L | Mab 44B1 light chain | protein | 212 | 7% helix, 54% strand | — |
Ligands and binding sites
- GN1 · 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · 3 copies · chains A, C, H
- GN4 · 2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · 3 copies · chains A, B, C, D, H, L
- CL · Chloride ion · ion · 2 copies · chains C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.74 | 0.78 | 88 | empty |
| 2 | 809 | 0.73 | 0.78 | 89 | empty |
| 3 | 818 | 0.71 | 0.77 | 70 | empty |
| 4 | 697 | 0.69 | 0.77 | 69 | empty |
| 5 | 119 | 0.48 | 0.80 | 31 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2009 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 1990 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1957 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 320 Ų buried · 3 hydrogen bonds · protein-protein
- C–L · 293 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5DQ9 · Structure of S55-3 Fab in complex with Lipid A · 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 5DQ9 · PDBe 5DQ9
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