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Crystal structure of human prorenin
Analyse Crystal structure of human prorenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VCM
- Type
- protein
- Length
- 723 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prorenin
- EC
- 3.4.23.15
- UniProt
- P00797
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prorenin (EC 3.4.23.15) | protein | 335 | 13% helix, 40% strand | P00797 |
| B | Prorenin (EC 3.4.23.15) | protein | 325 | 14% helix, 39% strand | P00797 |
| P | Prorenin (EC 3.4.23.15) | protein | 38 | 32% helix, 18% strand | P00797 |
| Q | Prorenin (EC 3.4.23.15) | protein | 25 | 28% helix, 28% strand | P00797 |
Ligands and binding sites
- 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
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.96 | 18 | empty |
| 2 | 471 | 0.68 | 0.79 | 71 | empty |
| 3 | 327 | 0.58 | 0.77 | 47 | empty |
| 4 | 207 | 0.53 | 0.78 | 32 | empty |
| 5 | 183 | 0.51 | 0.78 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–P · 2235 Ų buried · 32 hydrogen bonds · protein-protein
- B–Q · 1467 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 3 hydrogen bonds · protein-protein
- B–P · 365 Ų buried · 3 hydrogen bonds · protein-protein
- A–Q · 314 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3VCM · Crystal structure of human prorenin · 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 3VCM · PDBe 3VCM · UniProt P00797
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