MolNFT v1 · #61285 · protein + RNA
Crystal structure of rluf in complex with a 22 nucleotide RNA substrate
3DH3 · Ribosomal large subunit pseudouridine synthase F: “Crystal structure of rluf in complex with a 22 nucleotide RNA substrate”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #61285 on GenesisL1: 3D structure, binding…
- PDB
- 3DH3
- Type
- protein + RNA
- Length
- 1,047 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal large subunit pseudouridine synthase F; Stem loop fragment of E. COLI 23S RNA
- EC
- 5.4.99.-
- UniProt
- P32684
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal large subunit pseudouridine synthase F (EC 5.4.99.-) | protein | 240 | 24% helix, 27% strand | P32684 |
| E, F, G, H | Stem loop fragment of E. COLI 23S RNA | rna | 22 | — | — |
| B | Ribosomal large subunit pseudouridine synthase F (EC 5.4.99.-) | protein | 241 | 24% helix, 27% strand | P32684 |
| C, D | Ribosomal large subunit pseudouridine synthase F (EC 5.4.99.-) | protein | 239 | 24% helix, 27% strand | P32684 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.71 | 0.76 | 79 | empty |
| 2 | 800 | 0.65 | 0.74 | 68 | empty |
| 3 | 385 | 0.53 | 0.73 | 26 | empty |
| 4 | 202 | 0.47 | 0.75 | 31 | empty |
| 5 | 50 | 0.42 | 0.84 | 17 | empty |
Interfaces
10 interfaces between chains.
- D–H · 1793 Ų buried · 81 hydrogen bonds · protein-nucleic
- B–F · 1740 Ų buried · 74 hydrogen bonds · protein-nucleic
- C–G · 1732 Ų buried · 69 hydrogen bonds · protein-nucleic
- A–E · 1727 Ų buried · 74 hydrogen bonds · protein-nucleic
- B–C · 308 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3DH3 · Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate · the same entry in another collection · chain H against H, TM-score 1.00
- P32684 · AlphaFold monomer V2.0 prediction for dual-specificity RNA pseudouridine synthase rluf… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P32684
- Elsewhere: RCSB PDB 3DH3 · PDBe 3DH3 · UniProt P32684
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