MolNFT v1 · #144058 · protein
Trastuzumab Fab D185A (light chain) mutant.
6BHZ · Trastuzumab anti-HER2 Fab heavy chain: “Trastuzumab Fab D185A (light chain) mutant.”. X-ray diffraction, 10 pockets (best druggability 0.67). MolNFT v1 #144058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BHZ
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trastuzumab anti-HER2 Fab heavy chain; Trastuzumab anti-HER2 Fab light chain D185A
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Trastuzumab anti-HER2 Fab heavy chain | protein | 212 | 10% helix, 51% strand | — |
| L | Trastuzumab anti-HER2 Fab light chain D185A | protein | 213 | 6% helix, 52% strand | — |
| I | Trastuzumab anti-HER2 Fab heavy chain | protein | 206 | 9% helix, 53% strand | — |
| M | Trastuzumab anti-HER2 Fab light chain D185A | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains L, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.67 | 0.75 | 75 | empty |
| 2 | 394 | 0.57 | 0.75 | 48 | empty |
| 3 | 307 | 0.54 | 0.75 | 37 | empty |
| 4 | 92 | 0.33 | 0.73 | 20 | empty |
| 5 | 79 | 0.33 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1720 Ų buried · 14 hydrogen bonds · protein-protein
- I–M · 1601 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 686 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6BHZ · Trastuzumab Fab D185A (Light Chain) Mutant. · the same entry in another collection · chain H against H, 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 6BHZ · PDBe 6BHZ
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