MolNFT v1 · #67094 · protein + RNA
Crystal structure of RNase P /RNase mrp proteins POP6, POP7 in a complex with the P3 domain of RNase mrp RNA
3IAB · Ribonucleases P/MRP protein subunit POP6: “Crystal structure of RNase P /RNase mrp proteins POP6, POP7 in a complex with the P3 domain of RNase mrp RNA”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.66). MolNFT…
- PDB
- 3IAB
- Type
- protein + RNA
- Length
- 301 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleases P/MRP protein subunit POP6; Ribonucleases P/MRP protein subunit POP7; P3…
- EC
- 3.1.26.5
- UniProt
- P53218, P38291
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleases P/MRP protein subunit POP6 (EC 3.1.26.5) | protein | 148 | 29% helix, 31% strand | P53218 |
| B | Ribonucleases P/MRP protein subunit POP7 (EC 3.1.26.5) | protein | 107 | 36% helix, 36% strand | P38291 |
| R | P3 domain of the RNA component of RNase mrp (EC 3.1.26.5) | rna | 46 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.66 | 0.79 | 26 | empty |
| 2 | 241 | 0.48 | 0.74 | 29 | empty |
| 3 | 86 | 0.45 | 0.81 | 19 | empty |
| 4 | 68 | 0.37 | 0.78 | 11 | empty |
| 5 | 91 | 0.34 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–R · 1754 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–R · 974 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 906 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3IAB · Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3… · the same entry in another collection · chain A against A, TM-score 1.00
- P53218 · AlphaFold monomer V2.0 prediction for ribonucleases P/MRP protein subunit POP6 (P53218) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P38291 · AlphaFold monomer V2.0 prediction for ribonucleases P/MRP protein subunit POP7 (P38291) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P53218
- Every structure of UniProt P38291
- Elsewhere: RCSB PDB 3IAB · PDBe 3IAB · UniProt P53218 · UniProt P38291
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