MolNFT v1 · #136836 · protein
Room temperature (280K) crystal structure of KAPOSI'S sarcoma- associated herpesvirus protease in complex with allosteric inhibitor (compound 250)
5V5D · Orf 17: “Room temperature (280K) crystal structure of KAPOSI'S sarcoma- associated herpesvirus protease in complex…”. X-ray diffraction, 1 ligand (8OY), 4 pockets (best druggability 0.71). MolNFT v1 #136836 on GenesisL1: 3D…
- PDB
- 5V5D
- Type
- protein
- Length
- 377 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf 17
- UniProt
- O40922
- Ligands
- 8OY
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf 17 | protein | 191 | 30% helix, 26% strand | O40922 |
| B | Orf 17 | protein | 186 | 28% helix, 28% strand | O40922 |
Ligands and binding sites
- 8OY · 4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-(phenylamino)benzoic acid · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.71 | 0.78 | 60 | empty |
| 2 | 245 | 0.55 | 0.77 | 29 | 8OY |
| 3 | 133 | 0.46 | 0.76 | 14 | 8OY |
| 4 | 72 | 0.31 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 728 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5V5D · Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus… · 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 O40922
- Elsewhere: RCSB PDB 5V5D · PDBe 5V5D · UniProt O40922
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