Research workbench
Crystal structure of the Fab fragment of anti-CD20 antibody ofatumumab
Analyse Crystal structure of the Fab fragment of anti-CD20 antibody ofatumumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GIZ
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of anti-CD20 antibody ofatumumab, light chain; Fab fragment of anti-CD20…
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab fragment of anti-CD20 antibody ofatumumab, light chain | protein | 211 | 5% helix, 51% strand | — |
| H | Fab fragment of anti-CD20 antibody ofatumumab, heavy chain | protein | 216 | 7% helix, 51% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.59 | 0.75 | 45 | empty |
| 2 | 58 | 0.56 | 0.90 | 20 | empty |
| 3 | 129 | 0.41 | 0.75 | 20 | empty |
| 4 | 102 | 0.36 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- L–H · 1756 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3GIZ · Crystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab · 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 3GIZ · PDBe 3GIZ
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