MolNFT v1 · #118169 · protein
Cetuximab Fab in complex with L5E meditope variant
5ETU · Cetuximab Fab light chain: “Cetuximab Fab in complex with L5E meditope variant”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.74). MolNFT v1 #118169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ETU
- 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; L5E meditope variant
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| B | Cetuximab Fab heavy chain | protein | 216 | 6% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
| E, F | L5E meditope variant | 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
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 | 1090 | 0.74 | 0.77 | 113 | empty |
| 2 | 519 | 0.66 | 0.77 | 59 | PO4 |
| 3 | 372 | 0.60 | 0.77 | 46 | PO4 |
| 4 | 50 | 0.54 | 0.90 | 19 | empty |
| 5 | 73 | 0.49 | 0.84 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1686 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1669 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 537 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 536 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5ETU · Cetuximab Fab in complex with L5E meditope variant · the same entry in another collection · chain C against C, 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 5ETU · PDBe 5ETU
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