MolNFT v1 · #45999 · protein + RNA
Crystal structure of pseudoudirinde synthase trua in complex with leucyl tRNA
2NRE: “Crystal structure of pseudoudirinde synthase trua in complex with leucyl tRNA”. X-ray diffraction, 1 ligand (K), 4 pockets (best druggability 0.68). MolNFT v1 #45999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NRE
- Type
- protein + RNA
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl tRNA; TRNA pseudouridine synthase a
- EC
- 5.4.99.12
- UniProt
- P07649
- Ligands
- K
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Leucyl tRNA | rna | 56 | — | — |
| A | TRNA pseudouridine synthase a (EC 5.4.99.12) | protein | 259 | 21% helix, 20% strand | P07649 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.68 | 0.77 | 41 | empty |
| 2 | 541 | 0.61 | 0.75 | 50 | empty |
| 3 | 342 | 0.55 | 0.76 | 23 | empty |
| 4 | 79 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- F–A · 506 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2NRE · Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA · the same entry in another collection · chain F against F, TM-score 1.00
- P07649 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase a (P07649) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P07649
- Elsewhere: RCSB PDB 2NRE · PDBe 2NRE · UniProt P07649
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