MolNFT v1 · #139490 · protein
Crystal structure of trastuzumab Fab fragment bearing P-azido-L- phenylalanine
5XHF · Polypeptide (L chain): “Crystal structure of trastuzumab Fab fragment bearing P-azido-L- phenylalanine”. X-ray diffraction, 10 pockets (best druggability 0.65). MolNFT v1 #139490 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5XHF
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide (L chain); Polypeptide (H chain)
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polypeptide (L chain) | protein | 213 | 5% helix, 48% strand | — |
| B | Polypeptide (H chain) | protein | 214 | 6% helix, 51% strand | — |
| C | Polypeptide (L chain) | protein | 214 | 6% helix, 49% strand | — |
| D | Polypeptide (H chain) | protein | 220 | 4% helix, 51% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.65 | 0.75 | 68 | empty |
| 2 | 352 | 0.55 | 0.75 | 37 | empty |
| 3 | 296 | 0.51 | 0.74 | 43 | empty |
| 4 | 161 | 0.50 | 0.78 | 31 | empty |
| 5 | 122 | 0.40 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1984 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1817 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 719 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5XHF · Crystal structure of Trastuzumab Fab fragment bearing p-azido-L-phenylalanine · 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
- Elsewhere: RCSB PDB 5XHF · PDBe 5XHF
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