MolNFT v1 · #82630 · protein
Human renin in complex with compound 18
3VSX: “Human renin in complex with compound 18”. X-ray diffraction, 2 ligands (R32, NAG), 5 pockets (best druggability 0.82). MolNFT v1 #82630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VSX
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Renin
- EC
- 3.4.23.15
- UniProt
- P00797
- Ligands
- R32, NAG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 340 | 12% helix, 44% strand | P00797 |
Ligands and binding sites
- R32 · (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-2-(propan-2-yl)hexanamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.82 | 0.87 | 79 | empty |
| 2 | 648 | 0.76 | 0.81 | 63 | R32 |
| 3 | 680 | 0.76 | 0.81 | 72 | R32 |
| 4 | 312 | 0.55 | 0.76 | 34 | empty |
| 5 | 50 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1082 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 3VSX · Human renin in complex with compound 18 · 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 P00797
- Elsewhere: RCSB PDB 3VSX · PDBe 3VSX · UniProt P00797
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