MolNFT v1 · #31702 · protein + RNA
Crystal structure of staphylococcus aureus tRNA adenosine deaminase, tada, in complex with RNA
2B3J · Anticodon stem-loop of T-RNA-ARG2 (nucleotides 27-42): “Crystal structure of staphylococcus aureus tRNA adenosine deaminase, tada, in complex with RNA”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 2B3J
- Type
- protein + RNA
- Length
- 658 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anticodon stem-loop of T-RNA-ARG2 (nucleotides 27-42); TRNA adenosine deaminase
- EC
- 3.5.4.-
- UniProt
- Q99W51
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Anticodon stem-loop of T-RNA-ARG2 (nucleotides 27-42) | rna | 15 | — | — |
| G | Anticodon stem-loop of T-RNA-ARG2 (nucleotides 27-42) | rna | 8 | — | — |
| H | Anticodon stem-loop of T-RNA-ARG2 (nucleotides 27-42) | rna | 16 | — | — |
| A, B | TRNA adenosine deaminase (EC 3.5.4.-) | protein | 151 | 41% helix, 21% strand | Q99W51 |
| C | TRNA adenosine deaminase (EC 3.5.4.-) | protein | 152 | 43% helix, 21% strand | Q99W51 |
| D | TRNA adenosine deaminase (EC 3.5.4.-) | protein | 150 | 43% helix, 20% strand | Q99W51 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains E, A, F, B, G, C, H, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.70 | 0.76 | 91 | empty |
| 2 | 108 | 0.66 | 0.90 | 24 | GOL |
| 3 | 165 | 0.65 | 0.86 | 27 | GOL |
| 4 | 100 | 0.64 | 0.89 | 23 | GOL |
| 5 | 111 | 0.58 | 0.85 | 21 | GOL |
Interfaces
12 interfaces between chains.
- A–B · 1325 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1274 Ų buried · 13 hydrogen bonds · protein-protein
- H–D · 830 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–B · 799 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–A · 797 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2B3J · Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex… · the same entry in another collection · chain H against H, TM-score 1.00
- Q99W51 · AlphaFold monomer V2.0 prediction for tRNA-specific adenosine deaminase (Q99W51) · a predicted model of the same protein · chain A 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 Q99W51
- Elsewhere: RCSB PDB 2B3J · PDBe 2B3J · UniProt Q99W51
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