Research workbench
Structure of meditope enabled trastuzumab I83E variant
Analyse Structure of meditope enabled trastuzumab I83E variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U3D
- Type
- protein
- Length
- 552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Memab trastuzumab Fab light chain I83E; Memab trastuzumab Fab heavy chain; Protein L…
- UniProt
- Q51918, Q2UW42
- Ligands
- MRY
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Memab trastuzumab Fab light chain I83E | protein | 214 | 6% helix, 51% strand | — |
| B | Memab trastuzumab Fab heavy chain | protein | 221 | 10% helix, 52% strand | — |
| E | Protein L | protein | 63 | 35% helix, 44% strand | Q51918 |
| C | Immunoglobulin G binding protein a | protein | 54 | 78% helix, 2% strand | Q2UW42 |
Ligands and binding sites
- MRY · Meso-erythritol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.66 | 0.75 | 71 | empty |
| 2 | 142 | 0.56 | 0.82 | 25 | empty |
| 3 | 60 | 0.56 | 0.89 | 20 | empty |
| 4 | 91 | 0.40 | 0.77 | 23 | empty |
| 5 | 75 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2007 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 722 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 229 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5U3D · Structure of meditope enabled trastuzumab I83E variant · 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
- Every structure of UniProt Q51918
- Every structure of UniProt Q2UW42
- Elsewhere: RCSB PDB 5U3D · PDBe 5U3D · UniProt Q51918 · UniProt Q2UW42
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.