MolNFT v1 · #122025 · protein
Cetuximab Fab in complex with mpt-cys meditope
5ID1 · Cetuximab Fab light chain: “Cetuximab Fab in complex with mpt-cys meditope”. X-ray diffraction, 3 ligands (MPT, NAG, PO4), 11 pockets (best druggability 0.74). MolNFT v1 #122025 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5ID1
- Type
- protein
- Length
- 872 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
- MPT, 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 | 214 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 212 | 7% helix, 53% strand | — |
| E, F | Meditope | protein | 11 | 0% helix, 36% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 2 copies · chains C, E, A, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- PO4 · Phosphate ion · ion · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.74 | 0.77 | 94 | empty |
| 2 | 381 | 0.62 | 0.77 | 45 | PO4 |
| 3 | 390 | 0.62 | 0.77 | 42 | PO4 |
| 4 | 53 | 0.54 | 0.90 | 19 | empty |
| 5 | 246 | 0.52 | 0.76 | 42 | MPT |
Interfaces
7 interfaces between chains.
- A–B · 1694 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 709 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 503 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 502 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 5ID1 · Cetuximab Fab in complex with MPT-Cys 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 5ID1 · PDBe 5ID1
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