Research workbench
Cetuximab Fab in complex with CQFDA(PH)2STRRLKC
Analyse Cetuximab Fab in complex with CQFDA(PH)2STRRLKC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T1K
- 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; CQFDA(PH)2STRRLKC peptide
- Ligands
- MRY, PO4
- Pockets
- 11 · 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 | 213 | 6% helix, 51% strand | — |
| B | Cetuximab Fab heavy chain | protein | 218 | 7% helix, 51% strand | — |
| D | Cetuximab Fab heavy chain | protein | 215 | 7% helix, 52% strand | — |
| E, F | CQFDA(PH)2STRRLKC peptide | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.73 | 0.77 | 95 | empty |
| 2 | 415 | 0.63 | 0.78 | 52 | PO4 |
| 3 | 370 | 0.61 | 0.77 | 47 | PO4 |
| 4 | 183 | 0.50 | 0.77 | 37 | empty |
| 5 | 53 | 0.50 | 0.87 | 22 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1713 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1682 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 771 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 553 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 530 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 modified (disulfide, nonstandard, cyclization).
Compared structures
- 5T1K · Cetuximab Fab in complex with CQFDA(Ph)2STRRLKC · the same entry in another collection · chain A against A, 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 5T1K · PDBe 5T1K
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