Research workbench
Crystal structure of the humanized recombinant Fab fragment of a murine; antibody
Analyse Crystal structure of the humanized recombinant Fab fragment of a murine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AAZ
- Type
- protein
- Length
- 914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Humanized recombinant Fab fragment of a murine
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Humanized recombinant Fab fragment of a murine | protein | 228 | 5% helix, 51% strand | — |
| B | Humanized recombinant Fab fragment of a murine | protein | 229 | 7% helix, 48% strand | — |
| H | Humanized recombinant Fab fragment of a murine | protein | 229 | 5% helix, 51% strand | — |
| L | Humanized recombinant Fab fragment of a murine | protein | 228 | 6% helix, 48% strand | — |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.74 | 0.84 | 34 | empty |
| 2 | 364 | 0.70 | 0.82 | 45 | empty |
| 3 | 252 | 0.67 | 0.84 | 37 | empty |
| 4 | 268 | 0.62 | 0.80 | 36 | empty |
| 5 | 235 | 0.58 | 0.80 | 38 | empty |
Interfaces
6 interfaces between chains.
- H–L · 2206 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2162 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 509 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 369 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 152 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3AAZ · Crystal structure of the humanized recombinant Fab fragment of a murine; antibody · 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 3AAZ · PDBe 3AAZ
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