Research workbench
Crystal structure of staphylococcus aureus tRNA adenosine deaminase, tada, in complex with RNA
Analyse Crystal structure of staphylococcus aureus tRNA adenosine deaminase, tada, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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