MolNFT v1 · #109513 · protein
Retrofitting antibodies with stabilizing mutations. herceptin scfv mutant.
4X4X · Human variable heavy chain of herceptin: “Retrofitting antibodies with stabilizing mutations. herceptin scfv mutant.”. X-ray diffraction, 5 pockets (best druggability 0.52). MolNFT v1 #109513 on GenesisL1: 3D structure, binding…
- PDB
- 4X4X
- Type
- protein
- Length
- 434 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human variable heavy chain of herceptin; Human variable light chain of herceptin
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human variable heavy chain of herceptin | protein | 118 | 8% helix, 53% strand | — |
| B | Human variable light chain of herceptin | protein | 106 | 3% helix, 47% strand | — |
| C | Human variable heavy chain of herceptin | protein | 112 | 5% helix, 53% strand | — |
| D | Human variable light chain of herceptin | protein | 98 | 3% helix, 51% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.52 | 0.84 | 25 | empty |
| 2 | 58 | 0.32 | 0.76 | 14 | empty |
| 3 | 60 | 0.29 | 0.74 | 17 | empty |
| 4 | 60 | 0.27 | 0.73 | 17 | empty |
| 5 | 53 | 0.25 | 0.72 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 771 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 651 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 620 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4X4X · Retrofitting antibodies with stabilizing mutations. Herceptin scFv mutant. · 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 4X4X · PDBe 4X4X
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