Research workbench
Cetuximab Fab in complex with CQA(PH)2DLSTRRLKC peptide
Analyse Cetuximab Fab in complex with CQA(PH)2DLSTRRLKC peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T1L
- Type
- protein
- Length
- 882 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 CQA(PH)2DLSTRRLKC
- Ligands
- NAG, PO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% 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 | 216 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
| E, F | Cyclic meditope CQA(PH)2DLSTRRLKC | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.74 | 0.77 | 102 | empty |
| 2 | 405 | 0.63 | 0.78 | 42 | PO4 |
| 3 | 389 | 0.62 | 0.77 | 41 | PO4 |
| 4 | 267 | 0.56 | 0.77 | 46 | empty |
| 5 | 225 | 0.51 | 0.76 | 37 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1689 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1683 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 780 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 543 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 539 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 modified, 2 glycan (disulfide, N-glycosylation, nonstandard, cyclization).
Compared structures
- 5T1L · Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide · 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 5T1L · PDBe 5T1L
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