MolNFT v1 · #121545 · protein
Cetuximab Fab in complex with amidated meditope
5HYQ · Cetuximab light chain: “Cetuximab Fab in complex with amidated meditope”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.75). MolNFT v1 #121545 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HYQ
- Type
- protein
- Length
- 883 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab light chain; Cetuximab heavy chain; Amidated meditope
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab light chain | protein | 213 | 6% helix, 50% strand | — |
| B | Cetuximab heavy chain | protein | 220 | 7% helix, 52% strand | — |
| D | Cetuximab heavy chain | protein | 213 | 7% helix, 52% strand | — |
| E, F | Amidated meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.75 | 0.77 | 98 | empty |
| 2 | 367 | 0.62 | 0.78 | 43 | PO4 |
| 3 | 375 | 0.61 | 0.77 | 42 | PO4 |
| 4 | 251 | 0.54 | 0.76 | 44 | empty |
| 5 | 223 | 0.51 | 0.76 | 43 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1843 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1673 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 781 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 534 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 506 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5HYQ · Cetuximab Fab in complex with amidated meditope · 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 5HYQ · PDBe 5HYQ
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