MolNFT v1 · #109514 · protein
Retrofitting antibodies with stabilizing mutations. herceptin vl mutant F53D.
4X4Z · Herceptin vl domain with F53D mutation: “Retrofitting antibodies with stabilizing mutations. herceptin vl mutant F53D.”. X-ray diffraction, 3 pockets (best druggability 0.38). MolNFT v1 #109514 on GenesisL1: 3D structure, binding…
- PDB
- 4X4Z
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Herceptin vl domain with F53D mutation
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Herceptin vl domain with F53D mutation | protein | 106 | 3% helix, 51% strand | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.38 | 0.76 | 19 | empty |
| 2 | 66 | 0.32 | 0.75 | 17 | empty |
| 3 | 56 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4X4Z · Retrofitting antibodies with stabilizing mutations. Herceptin VL mutant F53D. · 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 4X4Z · PDBe 4X4Z
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