MolNFT v1 · #45987 · protein + RNA
Crystal structure of pseudoudirinde synthase trua in complex with leucyl tRNA
2NR0: “Crystal structure of pseudoudirinde synthase trua in complex with leucyl tRNA”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #45987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NR0
- Type
- protein + RNA
- Length
- 1,338 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Leucyl tRNA | rna | 80 | — | — |
| F | Leucyl tRNA | rna | 72 | — | — |
| G | Leucyl tRNA | rna | 67 | — | — |
| H | Leucyl tRNA | rna | 63 | — | — |
| A, B, C, D | TRNA pseudouridine synthase a (EC 5.4.99.12) | protein | 264 | 22% helix, 27% strand | P07649 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.80 | 0.90 | 44 | empty |
| 2 | 880 | 0.78 | 0.82 | 68 | empty |
| 3 | 433 | 0.74 | 0.84 | 36 | empty |
| 4 | 1137 | 0.72 | 0.77 | 65 | empty |
| 5 | 810 | 0.72 | 0.77 | 57 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1472 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1440 Ų buried · 8 hydrogen bonds · protein-protein
- F–B · 1122 Ų buried · 34 hydrogen bonds · protein-nucleic
- G–C · 1100 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–A · 710 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 2NR0 · Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA · the same entry in another collection · chain D against D, 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 0.98
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 2NR0 · PDBe 2NR0 · UniProt P07649
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