Research workbench
Crystal structure of MCPIP1 conserved domain with magnesium ion in the catalytic center
Analyse Crystal structure of MCPIP1 conserved domain with magnesium ion in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V34
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease ZC3H12A
- EC
- 3.1.-.-
- UniProt
- Q5D1E8
- Ligands
- MG
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease ZC3H12A (EC 3.1.-.-) | protein | 157 | 41% helix, 21% strand | Q5D1E8 |
| B | Ribonuclease ZC3H12A (EC 3.1.-.-) | protein | 158 | 41% helix, 20% strand | Q5D1E8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.69 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 240 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3V34 · Crystal structure of MCPIP1 conserved domain with magnesium ion in the catalytic center · the same entry in another collection · chain A against A, TM-score 1.00
- Q5D1E8 · AlphaFold monomer V2.0 prediction for endoribonuclease ZC3H12A (Q5D1E8) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q5D1E8
- Elsewhere: RCSB PDB 3V34 · PDBe 3V34 · UniProt Q5D1E8
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