Research workbench
Crystal structure of Fab667 complex
Analyse Crystal structure of Fab667 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PBW
- Type
- protein
- Length
- 440 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.058
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Fab667 light chain; Fab667 heavy chain; NPNANPNANPNA peptide
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · resolution 2.058 · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Fab667 light chain | protein | 211 | 7% helix, 51% strand | — |
| D | Fab667 heavy chain | protein | 221 | 8% helix, 52% strand | — |
| E | NPNANPNANPNA peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.48 | 0.74 | 38 | empty |
| 2 | 60 | 0.36 | 0.79 | 17 | empty |
| 3 | 109 | 0.35 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1760 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 426 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 252 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PBW · Crystal structure of FAB667 complex · the same entry in another collection · chain C against C, 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 6PBW · PDBe 6PBW
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