MolNFT v1 · #88878 · protein
Crystal structure of HIV-1 nef fyn-SH3 R96W variant
4D8D · Tyrosine-protein kinase fyn: “Crystal structure of HIV-1 nef fyn-SH3 R96W variant”. X-ray diffraction, 5 pockets (best druggability 0.56). MolNFT v1 #88878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D8D
- Type
- protein
- Length
- 326 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase fyn; Protein nef
- EC
- 2.7.10.2
- UniProt
- P06241, P03406
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 57 | 5% helix, 47% strand | P06241 |
| B | Protein nef | protein | 106 | 39% helix, 15% strand | P03406 |
| C | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 58 | 5% helix, 47% strand | P06241 |
| D | Protein nef | protein | 105 | 39% helix, 15% strand | P03406 |
Ligands and binding sites
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.56 | 0.79 | 25 | empty |
| 2 | 216 | 0.47 | 0.74 | 28 | empty |
| 3 | 103 | 0.41 | 0.77 | 16 | empty |
| 4 | 79 | 0.35 | 0.75 | 17 | empty |
| 5 | 62 | 0.32 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 736 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 647 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P06241
- Every structure of UniProt P03406
- Elsewhere: RCSB PDB 4D8D · PDBe 4D8D · UniProt P06241 · UniProt P03406
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