MolNFT v1 · #177134 · protein
Crystal structure of proteinaceous RNase P (prorp) from planctomycetes bacterium GWF2_40_8
7E8K · RNA-free ribonuclease P: “Crystal structure of proteinaceous RNase P (prorp) from planctomycetes bacterium GWF2_40_8”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.76). MolNFT v1 #177134 on GenesisL1: 3D…
- PDB
- 7E8K
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-free ribonuclease P
- EC
- 3.1.26.5
- UniProt
- A0A1G2XP69
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 199 | 60% helix, 11% strand | A0A1G2XP69 |
| B | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 205 | 62% helix, 10% strand | A0A1G2XP69 |
| D | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 200 | 64% helix, 11% strand | A0A1G2XP69 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.76 | 0.80 | 59 | SO4 |
| 2 | 888 | 0.75 | 0.79 | 60 | SO4 |
| 3 | 146 | 0.47 | 0.77 | 17 | empty |
| 4 | 145 | 0.44 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1735 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1682 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1622 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7E8K · Crystal structure of Proteinaceous RNase P (PRORP) from Planctomycetes bacterium GWF2_40_8 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1G2XP69
- Elsewhere: RCSB PDB 7E8K · PDBe 7E8K · UniProt A0A1G2XP69
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