MolNFT v1 · #122024 · protein
Cetuximab Fab in complex with aminoheptanoic acid-linked meditope
5ID0 · Cetuximab Fab light chain: “Cetuximab Fab in complex with aminoheptanoic acid-linked meditope”. X-ray diffraction, 3 ligands (011, NAG, PO4), 11 pockets (best druggability 0.74). MolNFT v1 #122024 on GenesisL1: 3D structure, binding…
- PDB
- 5ID0
- Type
- protein
- Length
- 876 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; Cyclic meditope
- Ligands
- 011, NAG, PO4
- Pockets
- 11 · 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, 51% 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 | Cyclic meditope | protein | 10 | 0% helix, 40% strand | — |
Ligands and binding sites
- 011 · 7-aminoheptanoic acid · ligand · 2 copies · chains A, E, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.74 | 0.77 | 115 | 011 |
| 2 | 376 | 0.63 | 0.78 | 47 | PO4 |
| 3 | 370 | 0.62 | 0.77 | 46 | PO4 |
| 4 | 74 | 0.51 | 0.85 | 22 | empty |
| 5 | 197 | 0.45 | 0.74 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1827 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 735 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 469 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 438 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 2 modified, 1 glycan (disulfide, covalent ligand, cyclization, N-glycosylation).
Compared structures
- 5ID0 · Cetuximab Fab in complex with aminoheptanoic acid-linked 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 5ID0 · PDBe 5ID0
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