Research workbench
Retrofitted antibodies with stabilizing mutations: herceptin scfv mutant with vh K30D and vl S52D.
Analyse Retrofitted antibodies with stabilizing mutations: herceptin scfv mutant with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DN0
- Type
- protein
- Length
- 447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human variable heavy chain of herceptin containing vh mutation K30D; Human variable light…
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human variable heavy chain of herceptin containing vh mutation K30D | protein | 119 | 8% helix, 51% strand | — |
| B, D | Human variable light chain of herceptin containing vl mutation S52D | protein | 106 | 3% helix, 49% strand | — |
| C | Human variable heavy chain of herceptin containing vh mutation K30D | protein | 116 | 5% helix, 55% strand | — |
Ligands and binding sites
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.64 | 0.80 | 42 | empty |
| 2 | 265 | 0.58 | 0.79 | 38 | empty |
| 3 | 75 | 0.40 | 0.79 | 18 | empty |
| 4 | 78 | 0.30 | 0.73 | 15 | FMT |
| 5 | 83 | 0.30 | 0.72 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 779 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 709 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6DN0 · Retrofitted antibodies with stabilizing mutations: Herceptin scFv mutant with VH K30D and… · 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 6DN0 · PDBe 6DN0
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