MolNFT v1 · #144059 · protein
Trastuzumab Fab N158A, D185A, K190A (light chain) triple mutant.
6BI0 · Trastuzumab anti-HER2 Fab heavy chain: “Trastuzumab Fab N158A, D185A, K190A (light chain) triple mutant.”. X-ray diffraction, 7 pockets (best druggability 0.65). MolNFT v1 #144059 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6BI0
- Type
- protein
- Length
- 844 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
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Trastuzumab anti-HER2 Fab heavy chain | protein | 212 | 11% helix, 52% strand | — |
| L | Trastuzumab anti-HER2 Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| I | Trastuzumab anti-HER2 Fab heavy chain | protein | 207 | 9% helix, 54% strand | — |
| M | Trastuzumab anti-HER2 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains H, L, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.65 | 0.75 | 68 | empty |
| 2 | 412 | 0.58 | 0.74 | 48 | EDO |
| 3 | 338 | 0.54 | 0.74 | 39 | empty |
| 4 | 151 | 0.42 | 0.74 | 27 | empty |
| 5 | 96 | 0.36 | 0.74 | 15 | EDO |
Interfaces
3 interfaces between chains.
- H–L · 1730 Ų buried · 12 hydrogen bonds · protein-protein
- I–M · 1603 Ų buried · 12 hydrogen bonds · protein-protein
- H–I · 688 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6BI0 · Trastuzumab Fab N158A, D185A, K190A (Light Chain) Triple 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 6BI0 · PDBe 6BI0
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