MolNFT v1 · #78966 · protein
Crystal structure of human mitochondrial RNA polymerase
3SPA · DNA-directed RNA polymerase, mitochondrial: “Crystal structure of human mitochondrial RNA polymerase”. X-ray diffraction, 2 ligands (CL, SO4), 13 pockets (best druggability 0.78). MolNFT v1 #78966 on GenesisL1: 3D structure, binding…
- PDB
- 3SPA
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase, mitochondrial; Nonamer peptide
- EC
- 2.7.7.6
- UniProt
- O00411
- Ligands
- CL, SO4
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase, mitochondrial (EC 2.7.7.6) | protein | 941 | 60% helix, 8% strand | O00411 |
| B | Nonamer peptide | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.78 | 0.82 | 62 | SO4 |
| 2 | 412 | 0.75 | 0.85 | 41 | empty |
| 3 | 422 | 0.75 | 0.84 | 37 | empty |
| 4 | 306 | 0.71 | 0.84 | 45 | empty |
| 5 | 333 | 0.71 | 0.84 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 312 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SPA · Crystal Structure of Human Mitochondrial RNA Polymerase · the same entry in another collection · chain A against A, TM-score 1.00
- O00411 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase, mitochondrial (O00411) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O00411
- Elsewhere: RCSB PDB 3SPA · PDBe 3SPA · UniProt O00411
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