MolNFT v1 · #145513 · protein
RNase P protein from thermotoga maritima in complex with 1-(4- fluorophenyl)-2-thiourea
6CQC · Ribonuclease P protein component: “RNase P protein from thermotoga maritima in complex with 1-(4- fluorophenyl)-2-thiourea”. X-ray diffraction, 2 ligands (8P4, SO4), 2 pockets (best druggability 0.63). MolNFT v1 #145513 on…
- PDB
- 6CQC
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease P protein component
- EC
- 3.1.26.5
- UniProt
- Q9X1H4
- Ligands
- 8P4, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease P protein component (EC 3.1.26.5) | protein | 109 | 48% helix, 20% strand | Q9X1H4 |
| B, C, D | Ribonuclease P protein component (EC 3.1.26.5) | protein | 107 | 50% helix, 21% strand | Q9X1H4 |
Ligands and binding sites
- 8P4 · 1-(4-fluorophenyl)thiourea · ligand · chains D
- SO4 · Sulfate ion · ion · 15 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.63 | 0.78 | 41 | SO4 |
| 2 | 320 | 0.59 | 0.77 | 37 | SO4 |
Interfaces
3 interfaces between chains.
- A–D · 688 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CQC · RNase P protein from Thermotoga maritima in complex with 1-(4-Fluorophenyl)-2-thiourea · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1H4 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component (Q9X1H4) · 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 Q9X1H4
- Elsewhere: RCSB PDB 6CQC · PDBe 6CQC · UniProt Q9X1H4
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