Research workbench
Cetuximab Fab in complex with cqfdlstrrlrcggsk meditope
Analyse Cetuximab Fab in complex with cqfdlstrrlrcggsk meditope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICX
- Type
- protein
- Length
- 880 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
- NAG, PO4
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| B | Cetuximab Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 212 | 7% helix, 53% strand | — |
| E, F | Meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- PO4 · Phosphate ion · ion · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.74 | 0.77 | 89 | empty |
| 2 | 361 | 0.61 | 0.77 | 39 | empty |
| 3 | 366 | 0.60 | 0.77 | 49 | empty |
| 4 | 235 | 0.51 | 0.76 | 44 | empty |
| 5 | 113 | 0.43 | 0.77 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1776 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1661 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 784 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 551 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 522 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified, 1 glycan (disulfide, nonstandard, N-glycosylation).
Compared structures
- 5ICX · Cetuximab Fab in complex with CQFDLSTRRLRCGGSK meditope · 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 5ICX · PDBe 5ICX
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