MolNFT v1 · #156095 · protein + RNA
Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncrna rmrp
6LT7 · Ribonuclease P protein subunit P20: “Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncrna rmrp”. X-ray diffraction, 7 pockets (best druggability 0.74). MolNFT v1 #156095 on GenesisL1: 3D structure…
- PDB
- 6LT7
- Type
- protein + RNA
- Length
- 578 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease P protein subunit P20; Ribonuclease P protein subunit P25; 50-mer RNA
- EC
- 3.1.26.5
- UniProt
- O75817, Q9BUL9
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribonuclease P protein subunit P20 (EC 3.1.26.5) | protein | 124 | 22% helix, 35% strand | O75817 |
| B | Ribonuclease P protein subunit P25 (EC 3.1.26.5) | protein | 116 | 26% helix, 36% strand | Q9BUL9 |
| C, F | 50-mer RNA | rna | 49 | — | — |
| E | Ribonuclease P protein subunit P25 (EC 3.1.26.5) | protein | 116 | 26% helix, 34% strand | Q9BUL9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, E, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.74 | 0.77 | 83 | EDO |
| 2 | 563 | 0.73 | 0.81 | 34 | empty |
| 3 | 601 | 0.72 | 0.81 | 48 | empty |
| 4 | 675 | 0.68 | 0.77 | 46 | empty |
| 5 | 582 | 0.64 | 0.76 | 38 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1788 Ų buried · 37 hydrogen bonds · protein-nucleic
- D–F · 1706 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–C · 1094 Ų buried · 24 hydrogen bonds · protein-nucleic
- E–F · 1045 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–E · 800 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6LT7 · Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9BUL9 · AlphaFold monomer V2.0 prediction for ribonuclease P protein subunit P25 (Q9BUL9) · a predicted model of the same protein · chain B against A, TM-score 0.96
- O75817 · AlphaFold monomer V2.0 prediction for ribonuclease P protein subunit P20 (O75817) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 O75817
- Every structure of UniProt Q9BUL9
- Elsewhere: RCSB PDB 6LT7 · PDBe 6LT7 · UniProt O75817 · UniProt Q9BUL9
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