MolNFT v1 · #143407 · protein
Structure of cetuximab with aminoheptanoic acid-linked N-(3- aminopropyl)-L-arginine meditope variant
6AYN · Cetuximab Fab light chain: “Structure of cetuximab with aminoheptanoic acid-linked N-(3- aminopropyl)-L-arginine meditope variant”. X-ray diffraction, 1 ligand (011), 9 pockets (best druggability 0.74). MolNFT v1 #143407 on…
- PDB
- 6AYN
- Type
- protein
- Length
- 884 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; Cyclic meditope
- UniProt
- P01834, S6B291
- Ligands
- 011
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 212 | 6% helix, 51% strand | P01834 |
| B, D | Cetuximab Fab heavy chain | protein | 220 | 8% helix, 52% strand | S6B291 |
| E, F | Cyclic meditope | protein | 10 | 0% helix, 40% strand | — |
Ligands and binding sites
- 011 · 7-aminoheptanoic acid · ligand · chains A, F
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 | 999 | 0.74 | 0.77 | 124 | 011 |
| 2 | 337 | 0.60 | 0.78 | 45 | empty |
| 3 | 310 | 0.60 | 0.78 | 40 | empty |
| 4 | 129 | 0.43 | 0.76 | 26 | empty |
| 5 | 101 | 0.41 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1852 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1846 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 481 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 480 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 6AYN · Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-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 6AYN · PDBe 6AYN · UniProt P01834 · UniProt S6B291
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