MolNFT v1 · #183783 · protein
Crystal structure of the anti-pas Fab 1.2 in complex with its epitope peptide and the anti-kappa vhh domain
7O31 · Anti-pas Fab 1.2 chimeric light chain: “Crystal structure of the anti-pas Fab 1.2 in complex with its epitope peptide and the anti-kappa vhh domain”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #183783 on…
- PDB
- 7O31
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-pas Fab 1.2 chimeric light chain; Anti-pas Fab 1.2 chimeric heavy chain; Anti-kappa…
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-pas Fab 1.2 chimeric light chain | protein | 218 | 6% helix, 51% strand | — |
| H | Anti-pas Fab 1.2 chimeric heavy chain | protein | 221 | 8% helix, 52% strand | — |
| X | Anti-kappa vhh domain | protein | 124 | 5% helix, 50% strand | — |
| P | PAS#1 epitope peptide | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains L, X, P, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.65 | 0.75 | 65 | empty |
| 2 | 206 | 0.50 | 0.76 | 36 | empty |
| 3 | 58 | 0.44 | 0.84 | 21 | EDO |
| 4 | 106 | 0.37 | 0.74 | 18 | empty |
| 5 | 69 | 0.32 | 0.75 | 18 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1935 Ų buried · 17 hydrogen bonds · protein-protein
- L–X · 699 Ų buried · 14 hydrogen bonds · protein-protein
- L–P · 358 Ų buried · 5 hydrogen bonds · protein-protein
- H–P · 339 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7O31 · Crystal structure of the anti-PAS Fab 1.2 in complex with its epitope peptide and the… · the same entry in another collection · chain L against L, 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 7O31 · PDBe 7O31
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