MolNFT v1 · #122502 · protein
Cetuximab Fab in complex with 3-bromophenylalanine meditope variant
5IR1 · Cetuximab Fab light chain: “Cetuximab Fab in complex with 3-bromophenylalanine meditope variant”. X-ray diffraction, 2 ligands (NAG, PO4), 9 pockets (best druggability 0.71). MolNFT v1 #122502 on GenesisL1: 3D structure, binding…
- PDB
- 5IR1
- Type
- protein
- Length
- 890 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 variant
- Ligands
- NAG, PO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 213 | 7% helix, 50% strand | — |
| B, D | Cetuximab Fab heavy chain | protein | 220 | 9% helix, 51% strand | — |
| E, F | Meditope variant | 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 A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.71 | 0.77 | 91 | empty |
| 2 | 435 | 0.67 | 0.79 | 47 | PO4 |
| 3 | 389 | 0.65 | 0.79 | 45 | PO4 |
| 4 | 278 | 0.54 | 0.76 | 58 | empty |
| 5 | 176 | 0.51 | 0.78 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1842 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1778 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 693 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 489 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 470 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified, 1 glycan (disulfide, nonstandard, N-glycosylation).
Compared structures
- 5IR1 · Cetuximab Fab in complex with 3-bromophenylalanine 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 5IR1 · PDBe 5IR1
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