Research workbench
Crystal structure of I83E meditope-enabled trastuzumab with azido- meditope
Analyse Crystal structure of I83E meditope-enabled trastuzumab with azido- meditope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U5M
- Type
- protein
- Length
- 566 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Memab trastuzumab, light chain; Memab trastuzumab, heavy chain; Protein L; Immunoglobulin…
- UniProt
- Q51918, Q2UW42
- Ligands
- ACE, MRY
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Memab trastuzumab, light chain | protein | 214 | 7% helix, 51% strand | — |
| B | Memab trastuzumab, heavy chain | protein | 223 | 9% helix, 54% strand | — |
| E | Protein L | protein | 63 | 35% helix, 44% strand | Q51918 |
| C | Immunoglobulin G binding protein a | protein | 54 | 78% helix, 0% strand | Q2UW42 |
| D | Azido-PEG4-meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
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 | 410 | 0.60 | 0.76 | 47 | MRY |
| 2 | 162 | 0.59 | 0.83 | 28 | empty |
| 3 | 263 | 0.54 | 0.76 | 44 | empty |
| 4 | 192 | 0.46 | 0.75 | 32 | empty |
| 5 | 74 | 0.43 | 0.81 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2034 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 716 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 647 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 596 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 520 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 modified, 1 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 5U5M · Crystal structure of I83E meditope-enabled trastuzumab with azido-meditope · 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 5U5M · PDBe 5U5M · UniProt Q51918 · UniProt Q2UW42
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