MolNFT v1 · #183058 · protein + RNA
Crystal structure of ZC3H12C pin-ccch zn finger domain with RNA heptamer
7NDJ · Probable ribonuclease ZC3H12C: “Crystal structure of ZC3H12C pin-ccch zn finger domain with RNA heptamer”. X-ray diffraction, 2 ligands (NA, ZN), 3 pockets (best druggability 0.31). MolNFT v1 #183058 on GenesisL1: 3D structure…
- PDB
- 7NDJ
- Type
- protein + RNA
- Length
- 364 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ribonuclease ZC3H12C; RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
- EC
- 3.1.-.-
- UniProt
- Q5DTV4
- Ligands
- NA, ZN
- Pockets
- 3 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ribonuclease ZC3H12C (EC 3.1.-.-) | protein | 166 | 38% helix, 25% strand | Q5DTV4 |
| B | Probable ribonuclease ZC3H12C (EC 3.1.-.-) | protein | 192 | 38% helix, 22% strand | Q5DTV4 |
| C | RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3') | rna | 6 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 8 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.31 | 0.76 | 12 | empty |
| 2 | 69 | 0.28 | 0.72 | 14 | empty |
| 3 | 51 | 0.27 | 0.74 | 10 | empty |
Interfaces
2 interfaces between chains.
- B–C · 393 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 221 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7NDJ · Crystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA heptamer · the same entry in another collection · chain A against A, TM-score 1.00
- Q5DTV4 · AlphaFold monomer V2.0 prediction for probable ribonuclease ZC3H12C (Q5DTV4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5DTV4
- Elsewhere: RCSB PDB 7NDJ · PDBe 7NDJ · UniProt Q5DTV4
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