Research workbench
Cqyn meditope - cetuximab Fab
Analyse Cqyn meditope - cetuximab Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GW5
- Type
- protein
- Length
- 880 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Cqyn meditope
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| B | Fab heavy chain | protein | 216 | 9% helix, 52% strand | — |
| C | Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| D | Fab heavy chain | protein | 215 | 7% helix, 52% strand | — |
| E, F | Cqyn meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
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 | 1093 | 0.75 | 0.78 | 109 | empty |
| 2 | 393 | 0.61 | 0.77 | 49 | empty |
| 3 | 381 | 0.61 | 0.77 | 44 | empty |
| 4 | 55 | 0.48 | 0.86 | 22 | empty |
| 5 | 141 | 0.44 | 0.76 | 31 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1731 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1723 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 678 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 428 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 403 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4GW5 · cQYN meditope - Cetuximab Fab · 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 4GW5 · PDBe 4GW5
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