MolNFT v1 · #122023 · protein
Cetuximab Fab in complex with gqfdlstrrlkg peptide
5ICZ · Cetuximab Fab light chain: “Cetuximab Fab in complex with gqfdlstrrlkg peptide”. X-ray diffraction, 1 ligand (PO4), 10 pockets (best druggability 0.69). MolNFT v1 #122023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ICZ
- Type
- protein
- Length
- 879 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
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.69
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 | 7% helix, 50% strand | — |
| B | Cetuximab Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 213 | 7% helix, 52% strand | — |
| E, F | Meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.69 | 0.77 | 75 | empty |
| 2 | 398 | 0.63 | 0.77 | 42 | PO4 |
| 3 | 390 | 0.62 | 0.77 | 48 | PO4 |
| 4 | 260 | 0.56 | 0.77 | 47 | empty |
| 5 | 243 | 0.53 | 0.76 | 49 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1714 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1695 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 772 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 518 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 490 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5ICZ · Cetuximab Fab in complex with GQFDLSTRRLKG peptide · 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 5ICZ · PDBe 5ICZ
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