Research workbench
Crystal structure of 6S-98S fiv protease with lopinavir bound
Analyse Crystal structure of 6S-98S fiv protease with lopinavir bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OGQ
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiv protease
- EC
- 3.4.23.-
- UniProt
- P16088
- Ligands
- AB1
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fiv protease (EC 3.4.23.-) | protein | 112 | 8% helix, 51% strand | P16088 |
Ligands and binding sites
- AB1 · N-{1-benzyl-4-[2-(2,6-dimethyl-phenoxy)-acetylamino]-3-hydroxy-5-phenyl-pentyl}-3-methyl-2-(2-oxo-tetrahydro-pyrimidin-1-yl)-butyramide · ligand · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 507 | 0.75 | 0.83 | 41 | AB1 |
| 2 | 78 | 0.41 | 0.79 | 19 | empty |
| 3 | 58 | 0.37 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1776 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3OGQ · Crystal Structure of 6s-98S FIV Protease with Lopinavir bound · 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 P16088
- Elsewhere: RCSB PDB 3OGQ · PDBe 3OGQ · UniProt P16088
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