MolNFT v1 · #122421 · protein
Cetuximab Fab in complex with 4-bromophenylalanine meditope variant
5IOP · Cetuximab Fab, light chain: “Cetuximab Fab in complex with 4-bromophenylalanine meditope variant”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.73). MolNFT v1 #122421 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IOP
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab, light chain; Cetuximab Fab, heavy chain; Meditope variant
- Ligands
- PO4
- Pockets
- 8 · 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, 50% strand | — |
| B | Cetuximab Fab, heavy chain | protein | 215 | 7% helix, 52% strand | — |
| D | Cetuximab Fab, heavy chain | protein | 213 | 7% helix, 52% strand | — |
| E, F | Meditope variant | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.73 | 0.76 | 138 | empty |
| 2 | 406 | 0.63 | 0.78 | 45 | PO4 |
| 3 | 380 | 0.62 | 0.78 | 42 | PO4 |
| 4 | 101 | 0.44 | 0.79 | 30 | empty |
| 5 | 110 | 0.41 | 0.76 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1677 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1669 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 773 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 495 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 489 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5IOP · Cetuximab Fab in complex with 4-bromophenylalanine meditope variant · 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 5IOP · PDBe 5IOP
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