MolNFT v1 · #118130 · protein
Cetuximab Fab in complex with cyclic beta-alanine-linked meditope
5ESQ · Cetuximab Fab light chain: “Cetuximab Fab in complex with cyclic beta-alanine-linked meditope”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.68). MolNFT v1 #118130 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ESQ
- Type
- protein
- Length
- 875 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 beta-alanine-linked meditope
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| B | Cetuximab Fab heavy chain | protein | 215 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 212 | 7% helix, 53% strand | — |
| E | Cyclic beta-alanine-linked meditope | protein | 10 | 0% helix, 40% strand | — |
| F | Cyclic beta-alanine-linked meditope | protein | 12 | 0% helix, 33% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 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 | 676 | 0.68 | 0.76 | 74 | empty |
| 2 | 416 | 0.62 | 0.77 | 46 | PO4 |
| 3 | 374 | 0.61 | 0.77 | 44 | PO4 |
| 4 | 259 | 0.51 | 0.75 | 55 | empty |
| 5 | 201 | 0.50 | 0.76 | 35 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1706 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1687 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 743 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 490 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 460 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5ESQ · Cetuximab Fab in complex with cyclic beta-alanine-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 5ESQ · PDBe 5ESQ
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