Research workbench
Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea-fowl lysozyme
Analyse Crystal structure of a cross-reaction complex between Fab F9.13.7 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FBI
- Type
- protein
- Length
- 1,128 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 F9.13.7 Fab (light chain); IGG1 F9.13.7 Fab (heavy chain); Guinea fowl lysozyme
- EC
- 3.2.1.17
- UniProt
- P01868, P00704
- Pockets
- 11 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, P | IGG1 F9.13.7 Fab (light chain) | protein | 214 | 4% helix, 43% strand | — |
| H, Q | IGG1 F9.13.7 Fab (heavy chain) | protein | 221 | 5% helix, 48% strand | P01868 |
| X, Y | Guinea fowl lysozyme (EC 3.2.1.17) | protein | 129 | 37% helix, 10% strand | P00704 |
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.55 | 0.75 | 40 | empty |
| 2 | 110 | 0.49 | 0.80 | 23 | empty |
| 3 | 61 | 0.39 | 0.80 | 17 | empty |
| 4 | 90 | 0.37 | 0.75 | 16 | empty |
| 5 | 134 | 0.35 | 0.72 | 26 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1928 Ų buried · 19 hydrogen bonds · protein-protein
- P–Q · 1909 Ų buried · 11 hydrogen bonds · protein-protein
- Q–Y · 710 Ų buried · 17 hydrogen bonds · protein-protein
- H–X · 706 Ų buried · 13 hydrogen bonds · protein-protein
- P–Y · 273 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1FBI · Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea-fowl lysozyme · the same entry in another collection · chain Y against Y, TM-score 1.00
- P00704 · AlphaFold monomer V2.0 prediction for lysozyme C (P00704) · a predicted model of the same protein · chain X against A, TM-score 0.98
- P01868 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region secreted form (P01868) · a predicted model of the same protein · chain H against A, TM-score 0.48
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01868
- Every structure of UniProt P00704
- Elsewhere: RCSB PDB 1FBI · PDBe 1FBI · UniProt P01868 · UniProt P00704
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