Research workbench
Crystal structure of renin in complex with nvp-BBV031 (compound 6)
Analyse Crystal structure of renin in complex with nvp-BBV031 (compound 6) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GJB
- Type
- protein
- Length
- 670 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
- 0ME, NAG, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 335 | 15% helix, 44% strand | P00797 |
Ligands and binding sites
- 0ME · (3S)-N-(9H-xanthen-9-ylmethyl)piperidine-3-carboxamide · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.80 | 0.87 | 64 | 0ME, SO4 |
| 2 | 440 | 0.79 | 0.87 | 53 | 0ME, SO4 |
| 3 | 92 | 0.48 | 0.82 | 25 | empty |
| 4 | 124 | 0.43 | 0.77 | 20 | empty |
| 5 | 50 | 0.31 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 747 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GJB · Crystal structure of renin in complex with NVP-BBV031 (compound 6) · 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 4GJB · PDBe 4GJB · UniProt P00797
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