MolNFT v2 · #117144 · protein
Structure of unliganded S55-5 Fab
5DQJ · S55-5 Fab (IgG1 kappa) light chain: “Structure of unliganded S55-5 Fab”. X-ray diffraction at 2.61, 12 pockets (best druggability 0.77). MolNFT v2 #117144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DQJ
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.61
- Source
- Mus musculus
- Molecule
- S55-5 Fab (IgG1 kappa) light chain; S55-5 Fab (IgG1) heavy chain
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.61 · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | S55-5 Fab (IgG1 kappa) light chain | protein | 217 | 6% helix, 53% strand | — |
| H, A | S55-5 Fab (IgG1) heavy chain | protein | 222 | 7% helix, 50% strand | — |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.77 | 0.84 | 85 | empty |
| 2 | 256 | 0.56 | 0.78 | 41 | empty |
| 3 | 219 | 0.52 | 0.77 | 32 | empty |
| 4 | 59 | 0.43 | 0.82 | 15 | empty |
| 5 | 128 | 0.43 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- L–H · 2101 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 2033 Ų buried · 24 hydrogen bonds · protein-protein
- L–A · 367 Ų buried · 2 hydrogen bonds · protein-protein
- H–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
- H–A · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5DQJ · Structure of unliganded S55-5 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 5DQJ · PDBe 5DQJ
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