Research workbench
Structure of a mutant cetuximab Fab fragment
Analyse Structure of a mutant cetuximab Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ARP
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab mutant light CHAIN,UNCHARACTERIZED protein; Cetuximab mutant Fab heavy…
- UniProt
- Q8TCD0, P0DOX5
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Cetuximab mutant light CHAIN,UNCHARACTERIZED protein | protein | 213 | 6% helix, 51% strand | Q8TCD0 |
| D | Cetuximab mutant Fab heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain | protein | 217 | 8% helix, 51% strand | P0DOX5 |
| B | Cetuximab mutant Fab heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain | protein | 214 | 8% helix, 51% strand | P0DOX5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains C, D, A
- GOL · Glycerol · additive · 7 copies · chains C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.68 | 0.78 | 74 | empty |
| 2 | 669 | 0.65 | 0.75 | 71 | empty |
| 3 | 547 | 0.63 | 0.75 | 56 | empty |
| 4 | 56 | 0.52 | 0.88 | 21 | empty |
| 5 | 150 | 0.46 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1755 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1732 Ų buried · 17 hydrogen bonds · protein-protein
- C–A · 685 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6ARP · Structure of a mutant Cetuximab Fab fragment · 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
- Every structure of UniProt Q8TCD0
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 6ARP · PDBe 6ARP · UniProt Q8TCD0 · UniProt P0DOX5
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