MolNFT v1 · #122659 · protein
Cetuximab Fab in complex with ARG8CIR meditope variant
5IVZ · Cetuximab Fab, light chain: “Cetuximab Fab in complex with ARG8CIR meditope variant”. X-ray diffraction, 2 ligands (CIR, PO4), 10 pockets (best druggability 0.80). MolNFT v1 #122659 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IVZ
- Type
- protein
- Length
- 877 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
- 10 · best druggability 0.80
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 | 216 | 7% helix, 52% strand | — |
| D | Cetuximab Fab, heavy chain | protein | 213 | 8% helix, 53% strand | — |
| E, F | Meditope variant | protein | 11 | 0% helix, 36% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B, E, C, D, F
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.80 | 0.81 | 128 | CIR, PO4 |
| 2 | 460 | 0.67 | 0.79 | 50 | CIR, PO4 |
| 3 | 56 | 0.54 | 0.89 | 22 | empty |
| 4 | 152 | 0.48 | 0.77 | 37 | empty |
| 5 | 133 | 0.44 | 0.76 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1724 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1704 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 412 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 410 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 5IVZ · Cetuximab Fab in complex with Arg8Cir meditope variant · the same entry in another collection · chain E against E, 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 5IVZ · PDBe 5IVZ
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