Research workbench
HIV-1 SF2 nef in complex with the fyn SH3 R96I mutant
Analyse HIV-1 SF2 nef in complex with the fyn SH3 R96I mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D7S
- Type
- protein
- Length
- 328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein nef; Tyrosine-protein kinase fyn
- UniProt
- P03407, E5RFS5
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein nef | protein | 105 | 38% helix, 15% strand | P03407 |
| B | Protein nef | protein | 103 | 39% helix, 16% strand | P03407 |
| C | Tyrosine-protein kinase fyn | protein | 59 | 5% helix, 44% strand | E5RFS5 |
| D | Tyrosine-protein kinase fyn | protein | 61 | 5% helix, 44% strand | E5RFS5 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.39 | 0.73 | 19 | empty |
| 2 | 84 | 0.36 | 0.75 | 13 | empty |
| 3 | 75 | 0.33 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–D · 732 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7D7S · HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant · 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 P03407
- Every structure of UniProt E5RFS5
- Elsewhere: RCSB PDB 7D7S · PDBe 7D7S · UniProt P03407 · UniProt E5RFS5
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