MolNFT v1 · #122630 · protein
Cetuximab Fab in complex with ARG9CIR meditope variant
5IV2 · Cetuximab Fab, light chain: “Cetuximab Fab in complex with ARG9CIR meditope variant”. X-ray diffraction, 2 ligands (CIR, PO4), 11 pockets (best druggability 0.73). MolNFT v1 #122630 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IV2
- 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
- CIR, PO4
- Pockets
- 11 · best druggability 0.73
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 | 214 | 7% helix, 51% strand | — |
| E, F | Meditope variant | protein | 11 | 0% helix, 18% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, E, C, F
- 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.73 | 0.77 | 106 | CIR |
| 2 | 390 | 0.63 | 0.78 | 45 | PO4 |
| 3 | 369 | 0.62 | 0.78 | 45 | PO4 |
| 4 | 69 | 0.49 | 0.85 | 21 | empty |
| 5 | 175 | 0.48 | 0.76 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1678 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 772 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 441 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 426 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 5IV2 · Cetuximab Fab in complex with Arg9Cir 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 5IV2 · PDBe 5IV2
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