Research workbench
Fab fragment of a native monomer-selective antibody in complex with alpha-1-antitrypsin
Analyse Fab fragment of a native monomer-selective antibody in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HX4
- Type
- protein
- Length
- 1,522 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.95
- Source
- Homo sapiens; Mus musculus
- Molecule
- Alpha-1-antitrypsin; Fab 1D9 heavy chain; Fab 1D9 light chain
- UniProt
- P01009
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.95 · 6 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1-antitrypsin | protein | 344 | 29% helix, 31% strand | P01009 |
| B | Alpha-1-antitrypsin | protein | 325 | 27% helix, 32% strand | P01009 |
| H | Fab 1D9 heavy chain | protein | 222 | 4% helix, 54% strand | — |
| L | Fab 1D9 light chain | protein | 217 | 5% helix, 54% strand | — |
| I | Fab 1D9 heavy chain | protein | 204 | 3% helix, 55% strand | — |
| M | Fab 1D9 light chain | protein | 210 | 4% helix, 52% strand | — |
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.70 | 0.82 | 34 | empty |
| 2 | 382 | 0.66 | 0.80 | 32 | empty |
| 3 | 224 | 0.64 | 0.83 | 36 | empty |
| 4 | 459 | 0.63 | 0.76 | 51 | empty |
| 5 | 437 | 0.60 | 0.75 | 50 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1987 Ų buried · 9 hydrogen bonds · protein-protein
- I–M · 1864 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 785 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 728 Ų buried · 10 hydrogen bonds · protein-protein
- B–L · 237 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6HX4 · Fab fragment of a native monomer-selective antibody in complex with alpha-1-antitrypsin · the same entry in another collection · chain M against M, TM-score 1.00
- P01009 · AlphaFold monomer V2.0 prediction for alpha-1-antitrypsin (P01009) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P01009
- Elsewhere: RCSB PDB 6HX4 · PDBe 6HX4 · UniProt P01009
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