Research workbench
Cetuximab Fab in complex with F3H meditope variant
Analyse Cetuximab Fab in complex with F3H meditope variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EUK
- Type
- protein
- Length
- 882 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- MUS MUSCULUS, HOMO SAPIENS; SYNTHETIC CONSTRUCT
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; F3H meditope
- Ligands
- MRY, NAG, PO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.5 · 5 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cetuximab Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| B | Cetuximab Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| C | Cetuximab Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| D | Cetuximab Fab heavy chain | protein | 213 | 7% helix, 52% strand | — |
| E, F | F3H meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- MRY · Meso-erythritol · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.72 | 0.78 | 76 | empty |
| 2 | 374 | 0.61 | 0.77 | 46 | empty |
| 3 | 371 | 0.60 | 0.77 | 48 | empty |
| 4 | 61 | 0.47 | 0.85 | 21 | empty |
| 5 | 111 | 0.44 | 0.78 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1842 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1696 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 792 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 553 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 551 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5EUK · Cetuximab Fab in complex with F3H 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 5EUK · PDBe 5EUK
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