Research workbench
Structure of cetuximab with aminoheptanoic acid-linked N- carboxyethylarginine meditope variant
Analyse Structure of cetuximab with aminoheptanoic acid-linked N- carboxyethylarginine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AZL
- Type
- protein
- Length
- 879 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; Meditope
- UniProt
- P01834, S6B291
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 212 | 6% helix, 51% strand | P01834 |
| B | Cetuximab Fab heavy chain | protein | 220 | 8% helix, 52% strand | S6B291 |
| D | Cetuximab Fab heavy chain | protein | 215 | 7% helix, 53% strand | S6B291 |
| E, F | Meditope | protein | 10 | 0% helix, 40% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.73 | 0.77 | 160 | empty |
| 2 | 325 | 0.60 | 0.78 | 35 | empty |
| 3 | 337 | 0.59 | 0.77 | 46 | empty |
| 4 | 51 | 0.53 | 0.89 | 20 | empty |
| 5 | 67 | 0.49 | 0.85 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1849 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1703 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 727 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 508 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 474 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 6AZL · Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope… · the same entry in another collection · chain C against C, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain A against A, TM-score 0.49
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 P01834
- Every structure of UniProt S6B291
- Elsewhere: RCSB PDB 6AZL · PDBe 6AZL · UniProt P01834 · UniProt S6B291
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