Research workbench
Crystal structure of SIVMAC239 nef bound to an engineered hck SH3 domain
Analyse Crystal structure of SIVMAC239 nef bound to an engineered hck SH3 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NUH
- Type
- protein
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein nef; Tyrosine-protein kinase HCK,TYROSINE-protein kinase hck
- EC
- 2.7.10.2
- UniProt
- Q5QGG3, P08631
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein nef | protein | 126 | 37% helix, 15% strand | Q5QGG3 |
| B | Protein nef | protein | 131 | 35% helix, 15% strand | Q5QGG3 |
| C | Tyrosine-protein kinase HCK,TYROSINE-protein kinase hck (EC 2.7.10.2) | protein | 54 | 6% helix, 48% strand | P08631 |
| D | Tyrosine-protein kinase HCK,TYROSINE-protein kinase hck (EC 2.7.10.2) | protein | 55 | 5% helix, 47% strand | P08631 |
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 | 683 | 0.83 | 0.87 | 62 | empty |
| 2 | 73 | 0.34 | 0.75 | 15 | empty |
| 3 | 59 | 0.32 | 0.75 | 15 | empty |
| 4 | 72 | 0.32 | 0.75 | 18 | empty |
| 5 | 57 | 0.31 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–C · 676 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 658 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 596 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 297 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5NUH · Crystal structure of SIVmac239 Nef bound to an engineered Hck SH3 domain · 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 Q5QGG3
- Every structure of UniProt P08631
- Elsewhere: RCSB PDB 5NUH · PDBe 5NUH · UniProt Q5QGG3 · UniProt P08631
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.