Research workbench
Crystal structure of human renin in complex with a biphenylpipderidinylcarbinol
Analyse Crystal structure of human renin in complex with a biphenylpipderidinylcarbinol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VPM
- Type
- protein
- Length
- 669 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
- 9G7, NAG, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 334 | 14% helix, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 335 | 14% helix, 43% strand | P00797 |
Ligands and binding sites
- 9G7 · methyl [(4S)-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxy-4-{(3R)-1-[(piperidin-4-yl)acetyl]piperidin-3-yl}butyl]carbamate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.78 | 0.84 | 51 | 9G7 |
| 2 | 469 | 0.77 | 0.85 | 50 | 9G7 |
| 3 | 154 | 0.61 | 0.84 | 23 | empty |
| 4 | 52 | 0.35 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 534 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VPM · Crystal Structure of Human Renin in Complex with a biphenylpipderidinylcarbinol · 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 5VPM · PDBe 5VPM · UniProt P00797
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