Research workbench
The crystal structure of xmrv protease complexed with tl-3
Analyse The crystal structure of xmrv protease complexed with tl-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SLZ
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pro-pol polyprotein
- UniProt
- Q9E7M1
- Ligands
- 3TL, NA
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gag-pro-pol polyprotein | protein | 114 | 6% helix, 49% strand | Q9E7M1 |
Ligands and binding sites
- 3TL · benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate · ligand · chains A, B
- NA · Sodium ion · metal · chains A, B
- FMT · Formic acid · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.72 | 0.83 | 43 | 3TL |
| 2 | 55 | 0.31 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3SLZ · The crystal structure of XMRV protease complexed with TL-3 · 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 Q9E7M1
- Elsewhere: RCSB PDB 3SLZ · PDBe 3SLZ · UniProt Q9E7M1
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