Research workbench
crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix
Analyse crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XRA
- Type
- protein
- Length
- 641 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- HOMO SAPIENS; SYNTHETIC CONSTRUCT
- Molecule
- Transmembrane protein GP41; HK20, human monoclonal antibody heavy chain; HK20, human…
- UniProt
- P04578
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane protein GP41 | protein | 203 | 90% helix, 0% strand | P04578 |
| H | HK20, human monoclonal antibody heavy chain | protein | 223 | 7% helix, 50% strand | — |
| L | HK20, human monoclonal antibody light chain | protein | 215 | 6% helix, 49% strand | — |
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 | 553 | 0.61 | 0.74 | 55 | empty |
| 2 | 226 | 0.58 | 0.79 | 31 | empty |
| 3 | 206 | 0.56 | 0.79 | 23 | empty |
| 4 | 148 | 0.43 | 0.75 | 21 | empty |
| 5 | 145 | 0.42 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1920 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 790 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 268 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2XRA · Crystal structure of the HK20 Fab in complex with a GP41 mimetic 5- helix · 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 P04578
- Elsewhere: RCSB PDB 2XRA · PDBe 2XRA · UniProt P04578
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