Research workbench
Structure of cetuximab with aminoheptanoic acid-linked N-(3- hydroxypropyl)-L-arginine meditope variant
Analyse Structure of cetuximab with aminoheptanoic acid-linked N-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AZK
- Type
- protein
- Length
- 883 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
- 011, SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 212 | 6% helix, 50% strand | P01834 |
| B | Cetuximab Fab heavy chain | protein | 219 | 8% helix, 52% strand | S6B291 |
| D | Cetuximab Fab heavy chain | protein | 220 | 8% helix, 50% strand | S6B291 |
| E, F | Meditope | protein | 10 | 0% helix, 40% strand | — |
Ligands and binding sites
- 011 · 7-aminoheptanoic acid · ligand · 2 copies · chains A, E, C, F
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
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 | 980 | 0.73 | 0.76 | 115 | 011 |
| 2 | 345 | 0.61 | 0.78 | 39 | empty |
| 3 | 354 | 0.60 | 0.77 | 46 | empty |
| 4 | 57 | 0.46 | 0.85 | 21 | empty |
| 5 | 164 | 0.45 | 0.75 | 33 | 011 |
Interfaces
7 interfaces between chains.
- C–D · 1856 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1793 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 781 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 491 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 491 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 6AZK · Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine… · 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 6AZK · PDBe 6AZK · UniProt P01834 · UniProt S6B291
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