MolNFT v1 · #144061 · protein
Trastuzumab Fab D185A (light chain) mutant biotin conjugation.
6BI2 · Trastuzumab anti-HER2 Fab heavy chain: “Trastuzumab Fab D185A (light chain) mutant biotin conjugation.”. X-ray diffraction, 1 ligand (BTN), 11 pockets (best druggability 0.57). MolNFT v1 #144061 on GenesisL1: 3D structure, binding…
- PDB
- 6BI2
- Type
- protein
- Length
- 861 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
- Ligands
- BTN
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Trastuzumab anti-HER2 Fab heavy chain | protein | 222 | 8% helix, 54% strand | — |
| L | Trastuzumab anti-HER2 Fab light chain | protein | 213 | 7% helix, 52% strand | — |
| I | Trastuzumab anti-HER2 Fab heavy chain | protein | 212 | 7% helix, 54% strand | — |
| M | Trastuzumab anti-HER2 Fab light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · 2 copies · chains L, M
- EDO · 1,2-ethanediol · additive · 7 copies · chains H, L, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.57 | 0.74 | 48 | empty |
| 2 | 341 | 0.57 | 0.76 | 43 | empty |
| 3 | 254 | 0.56 | 0.77 | 35 | EDO |
| 4 | 366 | 0.56 | 0.74 | 40 | EDO |
| 5 | 56 | 0.52 | 0.88 | 23 | EDO |
Interfaces
3 interfaces between chains.
- H–L · 1809 Ų buried · 16 hydrogen bonds · protein-protein
- I–M · 1706 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 689 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 cofactor (disulfide, biotinylation).
Compared structures
- 6BI2 · Trastuzumab Fab D185A (Light Chain) Mutant Biotin Conjugation. · 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 6BI2 · PDBe 6BI2
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