MolNFT v1 · #120739 · protein
Crystal structure of regnase pin domain, form I
5H9V · Ribonuclease ZC3H12A: “Crystal structure of regnase pin domain, form I”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.61). MolNFT v1 #120739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H9V
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease ZC3H12A
- EC
- 3.1.-.-
- UniProt
- Q5D1E7
- Ligands
- NA
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease ZC3H12A (EC 3.1.-.-) | protein | 161 | 39% helix, 22% strand | Q5D1E7 |
| B | Ribonuclease ZC3H12A (EC 3.1.-.-) | protein | 158 | 40% helix, 25% strand | Q5D1E7 |
| C, D | Ribonuclease ZC3H12A (EC 3.1.-.-) | protein | 162 | 38% helix, 24% strand | Q5D1E7 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.61 | 0.79 | 42 | empty |
| 2 | 308 | 0.60 | 0.78 | 45 | empty |
| 3 | 236 | 0.49 | 0.74 | 33 | empty |
| 4 | 187 | 0.47 | 0.75 | 24 | empty |
| 5 | 66 | 0.27 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 951 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 896 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 422 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
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 Q5D1E7
- Elsewhere: RCSB PDB 5H9V · PDBe 5H9V · UniProt Q5D1E7
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