Research workbench
A Fab derived from ixekizumab
Analyse A Fab derived from ixekizumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NOV
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab heavy chain | protein | 212 | 8% helix, 51% strand | — |
| B | Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| D | Fab light chain | protein | 219 | 5% helix, 52% strand | — |
Ligands and binding sites
- 12P · Dodecaethylene glycol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.66 | 0.78 | 58 | 12P |
| 2 | 710 | 0.65 | 0.74 | 64 | empty |
| 3 | 669 | 0.63 | 0.74 | 69 | empty |
| 4 | 131 | 0.41 | 0.75 | 24 | empty |
| 5 | 56 | 0.40 | 0.82 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1716 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1692 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 646 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 419 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6NOV · A Fab derived from ixekizumab · 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 6NOV · PDBe 6NOV
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