Research workbench
Crystal structure of renin in complex with nvp-AMQ838 (compound 5)
Analyse Crystal structure of renin in complex with nvp-AMQ838 (compound 5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GJ5
- Type
- protein
- Length
- 663 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
- 0LR, NAG
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 332 | 16% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 331 | 15% helix, 45% strand | P00797 |
Ligands and binding sites
- 0LR · (3R,4R)-3-(naphthalen-2-ylmethoxy)-4-phenylpiperidine · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.87 | 0.88 | 123 | 0LR |
| 2 | 62 | 0.35 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GJ5 · Crystal structure of renin in complex with NVP-AMQ838 (compound 5) · 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 4GJ5 · PDBe 4GJ5 · UniProt P00797
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