Research workbench
Pinatuzumab Fab in complex with anti-kappa vhh domain
Analyse Pinatuzumab Fab in complex with anti-kappa vhh domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AND
- Type
- protein
- Length
- 545 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-kappa vhh domain; Pinatuzumab Fab heavy chain; Pinatuzumab Fab light chain
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Anti-kappa vhh domain | protein | 120 | 8% helix, 49% strand | — |
| H | Pinatuzumab Fab heavy chain | protein | 213 | 8% helix, 55% strand | — |
| L | Pinatuzumab Fab light chain | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.76 | 0.84 | 84 | empty |
| 2 | 59 | 0.56 | 0.90 | 21 | empty |
| 3 | 95 | 0.56 | 0.86 | 35 | empty |
| 4 | 287 | 0.54 | 0.75 | 33 | empty |
| 5 | 138 | 0.46 | 0.77 | 26 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1777 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 579 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6AND · Pinatuzumab Fab in complex with anti-Kappa VHH domain · the same entry in another collection · chain K against K, 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 6AND · PDBe 6AND
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