MolNFT v1 · #121248 · protein
Cetuximab Fab in complex with cyclic linked meditope
5HPM · Cetuximab Fab light chain: “Cetuximab Fab in complex with cyclic linked meditope”. X-ray diffraction, 2 ligands (CY3, NAG), 7 pockets (best druggability 0.72). MolNFT v1 #121248 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5HPM
- Type
- protein
- Length
- 878 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 amidated, acetylated linked…
- Ligands
- CY3, NAG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 7% 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 | 216 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
| E, F | Cyclic amidated, acetylated linked meditope | protein | 11 | 0% helix, 36% strand | — |
Ligands and binding sites
- CY3 · 2-amino-3-mercapto-propionamide · ligand · 2 copies · chains A, E, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.72 | 0.76 | 112 | CY3 |
| 2 | 371 | 0.62 | 0.78 | 48 | empty |
| 3 | 373 | 0.61 | 0.77 | 47 | empty |
| 4 | 243 | 0.51 | 0.75 | 51 | empty |
| 5 | 164 | 0.46 | 0.76 | 33 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1746 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1698 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 830 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 524 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 523 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 2 glycan, 2 modified (disulfide, covalent ligand, N-glycosylation, nonstandard).
Compared structures
- 5HPM · Cetuximab Fab in complex with cyclic 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 5HPM · PDBe 5HPM
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