MolNFT v1 · #92793 · protein
Crystal structure of renin in complex with nvp-BGQ311 (compound 12)
4GJD: “Crystal structure of renin in complex with nvp-BGQ311 (compound 12)”. X-ray diffraction, 3 ligands (0N0, NAG, SO4), 5 pockets (best druggability 0.82). MolNFT v1 #92793 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GJD
- Type
- protein
- Length
- 672 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
- 0N0, NAG, SO4
- Pockets
- 5 · best druggability 0.82
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 | 335 | 15% helix, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 337 | 16% helix, 45% strand | P00797 |
Ligands and binding sites
- 0N0 · (3S,5R)-N-{[9-(4-methoxybutyl)-9H-xanthen-9-yl]methyl}-5-{[(4-methylphenyl)sulfonyl]amino}piperidine-3-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · chains A
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 | 936 | 0.82 | 0.84 | 91 | SO4 |
| 2 | 640 | 0.74 | 0.81 | 58 | 0N0 |
| 3 | 568 | 0.72 | 0.80 | 47 | 0N0 |
| 4 | 299 | 0.58 | 0.77 | 33 | empty |
| 5 | 130 | 0.40 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4GJD · Crystal structure of renin in complex with NVP-BGQ311 (compound 12) · 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 4GJD · PDBe 4GJD · UniProt P00797
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