MolNFT v1 · #134355 · protein
Cetuximab Fab in complex with cqydlstrrlkc
5T1M · Cetuximab Fab light chain: “Cetuximab Fab in complex with cqydlstrrlkc”. X-ray diffraction, 2 ligands (NAG, PO4), 9 pockets (best druggability 0.73). MolNFT v1 #134355 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T1M
- Type
- protein
- Length
- 897 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; Cyclic peptide cqydlstrrlkc
- Ligands
- NAG, PO4
- Pockets
- 9 · 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 | 213 | 6% helix, 51% strand | — |
| B | Cetuximab Fab heavy chain | protein | 219 | 9% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
| E, F, H | Cyclic peptide cqydlstrrlkc | 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 · 6 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 | 1098 | 0.73 | 0.76 | 120 | empty |
| 2 | 414 | 0.62 | 0.77 | 46 | PO4 |
| 3 | 364 | 0.61 | 0.77 | 48 | PO4 |
| 4 | 286 | 0.54 | 0.76 | 53 | empty |
| 5 | 51 | 0.53 | 0.89 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1774 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1690 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 741 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 481 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 477 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 5T1M · Cetuximab Fab in complex with CQYDLSTRRLKC · 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 5T1M · PDBe 5T1M
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