MolNFT v1 · #177138 · protein + RNA
Crystal structure of proteinaceous RNase P(PRORP) from planctomycetes bacterium GWF2_40_8 complexed with escherichia COLI histidine pre- tRNA
7E8O · RNA-free ribonuclease P: “Crystal structure of proteinaceous RNase P(PRORP) from planctomycetes bacterium GWF2_40_8 complexed with…”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.67). MolNFT v1 #177138 on…
- PDB
- 7E8O
- Type
- protein + RNA
- Length
- 827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-free ribonuclease P; Histidine pre-tRNA
- EC
- 3.1.26.5
- UniProt
- A0A1G2XP69
- Ligands
- CA
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 194 | 58% helix, 9% strand | A0A1G2XP69 |
| B | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 191 | 62% helix, 11% strand | A0A1G2XP69 |
| C | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 189 | 57% helix, 9% strand | A0A1G2XP69 |
| D | RNA-free ribonuclease P (EC 3.1.26.5) | protein | 185 | 58% helix, 11% strand | A0A1G2XP69 |
| X | Histidine pre-tRNA | rna | 68 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.67 | 0.76 | 35 | empty |
| 2 | 610 | 0.64 | 0.75 | 42 | empty |
| 3 | 135 | 0.51 | 0.80 | 27 | empty |
| 4 | 138 | 0.48 | 0.78 | 23 | empty |
| 5 | 168 | 0.41 | 0.73 | 25 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2225 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2007 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1063 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 958 Ų buried · 3 hydrogen bonds · protein-protein
- A–X · 282 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 7E8O · 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 7E8O · PDBe 7E8O · UniProt A0A1G2XP69
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