Research workbench
Crystal structure of trastuzumab Fab fragment bearing ne-(O- azidobenzyloxycarbonyl)-L-lysine
Analyse Crystal structure of trastuzumab Fab fragment bearing ne-(O… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XHG
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLYPEPTIDE(L); POLYPEPTIDE(H)
- Ligands
- OAZ, SO4
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLYPEPTIDE(L) | protein | 213 | 6% helix, 51% strand | — |
| B | POLYPEPTIDE(H) | protein | 214 | 10% helix, 51% strand | — |
| C | POLYPEPTIDE(L) | protein | 214 | 6% helix, 50% strand | — |
| D | POLYPEPTIDE(H) | protein | 220 | 8% helix, 53% strand | — |
Ligands and binding sites
- OAZ · (2-azidophenyl)methyl hydrogen carbonate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.66 | 0.75 | 78 | SO4 |
| 2 | 237 | 0.56 | 0.78 | 31 | EDO, PEG |
| 3 | 337 | 0.55 | 0.75 | 40 | empty |
| 4 | 65 | 0.54 | 0.88 | 18 | empty |
| 5 | 303 | 0.52 | 0.74 | 32 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1789 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1738 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 715 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5XHG · Crystal structure of Trastuzumab Fab fragment bearing… · the same entry in another collection · chain B against B, 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 5XHG · PDBe 5XHG
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