MolNFT v1 · #50344 · protein + RNA
Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex
2RFK · Guide RNA 1: “Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.70). MolNFT v1 #50344 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2RFK
- Type
- protein + RNA
- Length
- 522 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guide RNA 1; Guide RNA 2; Target RNA; Probable tRNA pseudouridine synthase B; Ribosome…
- EC
- 5.4.99.-
- UniProt
- Q7LWY0, Q8U1R4, Q8U029
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Guide RNA 1 | rna | 21 | — | — |
| E | Guide RNA 2 | rna | 26 | — | — |
| F | Target RNA | rna | 14 | — | — |
| A | Probable tRNA pseudouridine synthase B (EC 5.4.99.-) | protein | 334 | 26% helix, 31% strand | Q7LWY0 |
| B | Ribosome biogenesis protein NOP10 | protein | 53 | 21% helix, 15% strand | Q8U1R4 |
| C | Small nucleolar rnp similar to GAR1 | protein | 74 | 4% helix, 41% strand | Q8U029 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.70 | 0.75 | 48 | empty |
| 2 | 745 | 0.68 | 0.76 | 63 | empty |
| 3 | 135 | 0.40 | 0.74 | 17 | empty |
| 4 | 84 | 0.37 | 0.77 | 15 | empty |
| 5 | 94 | 0.34 | 0.74 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1421 Ų buried · 18 hydrogen bonds · protein-protein
- E–A · 1257 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–C · 1036 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 705 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- D–F · 559 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2RFK · Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q7LWY0 · AlphaFold monomer V2.0 prediction for probable tRNA pseudouridine synthase B (Q7LWY0) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q8U1R4 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein NOP10 (Q8U1R4) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q7LWY0
- Every structure of UniProt Q8U1R4
- Every structure of UniProt Q8U029
- Elsewhere: RCSB PDB 2RFK · PDBe 2RFK · UniProt Q7LWY0 · UniProt Q8U1R4 · UniProt Q8U029
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