Research workbench
Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the GP41 scrambledfp-mper SCRHYB3K construct gigafgllgflaagskk-ahx-K656NEQELLELDKWASLWN671 soaked in ammonium sulfate
Analyse Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EGS
- Type
- protein
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2F5 Fab' light chain; 2F5 Fab' heavy chain; GP41 scrfp-mper construct
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2F5 Fab' light chain | protein | 213 | 6% helix, 51% strand | — |
| B | 2F5 Fab' heavy chain | protein | 216 | 6% helix, 51% strand | — |
| C | GP41 scrfp-mper construct | protein | 7 | 0% helix, 14% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.59 | 0.75 | 49 | empty |
| 2 | 60 | 0.28 | 0.74 | 15 | empty |
| 3 | 62 | 0.26 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1820 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 245 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3EGS · Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41… · 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 3EGS · PDBe 3EGS
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