Research workbench
Crystal structure of the anti-pas Fab 1.1 in complex with its epitope peptide
Analyse Crystal structure of the anti-pas Fab 1.1 in complex with its epitope peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O30
- Type
- protein
- Length
- 892 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-pas Fab 1.1 chimeric light chain; Anti-pas Fab 1.1 chimeric heavy chain; PAS#1…
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Anti-pas Fab 1.1 chimeric light chain | protein | 218 | 7% helix, 50% strand | — |
| H | Anti-pas Fab 1.1 chimeric heavy chain | protein | 220 | 7% helix, 50% strand | — |
| P, Q | PAS#1 epitope peptide | protein | 10 | 0% helix, 0% strand | — |
| B | Anti-pas Fab 1.1 chimeric heavy chain | protein | 216 | 7% helix, 50% strand | — |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.70 | 0.76 | 70 | empty |
| 2 | 376 | 0.70 | 0.82 | 48 | empty |
| 3 | 682 | 0.66 | 0.75 | 52 | empty |
| 4 | 314 | 0.57 | 0.76 | 40 | empty |
| 5 | 266 | 0.53 | 0.76 | 34 | empty |
Interfaces
12 interfaces between chains.
- L–H · 1945 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1845 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 377 Ų buried · 8 hydrogen bonds · protein-protein
- L–P · 312 Ų buried · 4 hydrogen bonds · protein-protein
- A–Q · 302 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 7O30 · Crystal structure of the anti-PAS Fab 1.1 in complex with its epitope peptide · 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 7O30 · PDBe 7O30
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