MolNFT v1 · #124837 · protein
Protease PR5-sqv
5KR2: “Protease PR5-sqv”. X-ray diffraction, 1 ligand (ROC), 3 pockets (best druggability 0.75). MolNFT v1 #124837 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KR2
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease PR5-sqv
- UniProt
- V5YAB1
- Ligands
- ROC
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease PR5-sqv | protein | 99 | 4% helix, 57% strand | V5YAB1 |
Ligands and binding sites
- ROC · (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.75 | 0.80 | 60 | ROC |
| 2 | 416 | 0.68 | 0.80 | 35 | ROC |
| 3 | 137 | 0.44 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1799 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1761 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KR2 · Protease PR5-SQV · 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 V5YAB1
- Elsewhere: RCSB PDB 5KR2 · PDBe 5KR2 · UniProt V5YAB1
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