MolNFT v1 · #92789 · protein
Crystal structure of renin in complex with GP055321 (compound 4)
4GJ9: “Crystal structure of renin in complex with GP055321 (compound 4)”. X-ray diffraction, 2 ligands (0M2, NAG), 3 pockets (best druggability 0.80). MolNFT v1 #92789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GJ9
- Type
- protein
- Length
- 668 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
- 0M2, NAG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 333 | 15% helix, 47% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 335 | 15% helix, 45% strand | P00797 |
Ligands and binding sites
- 0M2 · (2R)-1-(3,8-dihydrodibenzo[b,f]pyrrolo[3,4-d]azepin-2(1H)-yl)propan-2-ol · 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
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 | 582 | 0.80 | 0.85 | 62 | 0M2 |
| 2 | 452 | 0.78 | 0.86 | 49 | 0M2 |
| 3 | 107 | 0.39 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 704 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GJ9 · Crystal structure of renin in complex with GP055321 (compound 4) · 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 4GJ9 · PDBe 4GJ9 · UniProt P00797
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