Research workbench
Renin in complex with (4S)-4-isopropyl-4-methyl-6-oxo-1-(3-(2-oxo-4- phenylpyrrolidin-1-YL)BENZYL)TETRAHYDROPYRIMIDIN-2(1H)-iminium
Analyse Renin in complex with (4S)-4-isopropyl-4-methyl-6-oxo-1-(3-(2-oxo-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XX4
- Type
- protein
- Length
- 677 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
- 70Y, NAG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 339 | 16% helix, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 338 | 16% helix, 44% strand | P00797 |
Ligands and binding sites
- 70Y · (2Z,6S)-2-imino-6-methyl-3-{3-[(4R)-2-oxo-4-phenylpyrrolidin-1-yl]benzyl}-6-(propan-2-yl)tetrahydropyrimidin-4(1H)-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.81 | 0.87 | 63 | empty |
| 2 | 726 | 0.77 | 0.81 | 66 | 70Y |
| 3 | 559 | 0.75 | 0.82 | 49 | 70Y |
| 4 | 240 | 0.58 | 0.80 | 38 | empty |
| 5 | 287 | 0.55 | 0.76 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XX4 · Renin in complex with (4S)-4-isopropyl-4-methyl-6-oxo-1-(3-(2-oxo-4-phenylpyrrolidin-1-yl)… · the same entry in another collection · chain B against B, 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 4XX4 · PDBe 4XX4 · UniProt P00797
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