MolNFT v1 · #172077 · protein
HER2-binding scfv-Fab fusion 841
6ZQK · 841 heavy chain: “HER2-binding scfv-Fab fusion 841”. X-ray diffraction, 18 pockets (best druggability 0.83). MolNFT v1 #172077 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZQK
- Type
- protein
- Length
- 1,313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 841 heavy chain; 841 light chain
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 841 heavy chain | protein | 442 | 6% helix, 50% strand | — |
| B | 841 light chain | protein | 215 | 9% helix, 53% strand | — |
| C | 841 heavy chain | protein | 443 | 5% helix, 50% strand | — |
| D | 841 light chain | protein | 213 | 8% helix, 51% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.83 | 0.84 | 93 | EDO |
| 2 | 438 | 0.68 | 0.79 | 46 | EDO |
| 3 | 345 | 0.65 | 0.80 | 47 | EDO |
| 4 | 381 | 0.58 | 0.75 | 45 | EDO |
| 5 | 316 | 0.51 | 0.73 | 46 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2185 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2144 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 46 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6ZQK · HER2-binding scFv-Fab fusion 841 · 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 6ZQK · PDBe 6ZQK
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