Research workbench
Trastuzumab Fab V3 in complex with 5-phenyl meditope variant
Analyse Trastuzumab Fab V3 in complex with 5-phenyl meditope variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B9Y
- Type
- protein
- Length
- 566 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trastuzumab Fab light chain; Trastuzumab Fab heavy chain; Protein L; Immunoglobulin G…
- UniProt
- P01834, Q6GMX6, Q51918, Q2UW42
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trastuzumab Fab light chain | protein | 214 | 7% helix, 51% strand | P01834 |
| B | Trastuzumab Fab heavy chain | protein | 223 | 11% helix, 54% strand | Q6GMX6 |
| E | Protein L | protein | 63 | 35% helix, 44% strand | Q51918 |
| C | Immunoglobulin G binding protein a | protein | 54 | 78% helix, 0% strand | Q2UW42 |
| D | Meditope | protein | 12 | 0% helix, 33% strand | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.61 | 0.76 | 53 | empty |
| 2 | 169 | 0.56 | 0.81 | 28 | empty |
| 3 | 268 | 0.52 | 0.75 | 42 | empty |
| 4 | 112 | 0.39 | 0.75 | 26 | empty |
| 5 | 107 | 0.37 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1983 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 730 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 591 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 464 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6B9Y · Trastuzumab Fab v3 in complex with 5-phenyl meditope variant · the same entry in another collection · chain A against A, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain A against A, TM-score 0.50
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01834
- Every structure of UniProt Q6GMX6
- Every structure of UniProt Q51918
- Every structure of UniProt Q2UW42
- Elsewhere: RCSB PDB 6B9Y · PDBe 6B9Y · UniProt P01834 · UniProt Q6GMX6 · UniProt Q51918 · UniProt Q2UW42
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