Research workbench
Cqfd meditope
Analyse Cqfd meditope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GW1
- Type
- protein
- Length
- 890 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Cqfd meditope
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab light chain | protein | 212 | 7% helix, 51% strand | — |
| B | Fab heavy chain | protein | 221 | 10% helix, 52% strand | — |
| C | Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| D | Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| E, F | Cqfd meditope | protein | 12 | 0% helix, 33% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
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 | 1168 | 0.74 | 0.77 | 128 | empty |
| 2 | 405 | 0.63 | 0.78 | 50 | empty |
| 3 | 402 | 0.62 | 0.77 | 46 | empty |
| 4 | 296 | 0.54 | 0.75 | 58 | empty |
| 5 | 139 | 0.48 | 0.78 | 24 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1903 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1828 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 812 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 518 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 500 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4GW1 · cQFD 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 4GW1 · PDBe 4GW1
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