Research workbench
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in ccacca
Analyse Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X4T
- Type
- protein + RNA
- Length
- 1,834 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; G70A tRNA minihelix ending in ccacca; RNA (5'-D(P*CP*G)-3'); RNA…
- EC
- 2.7.7.72
- UniProt
- O28126
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Cca-adding enzyme (EC 2.7.7.72) | protein | 437 | 43% helix, 22% strand | O28126 |
| B | G70A tRNA minihelix ending in ccacca | rna | 34 | — | — |
| D | G70A tRNA minihelix ending in ccacca | rna | 30 | — | — |
| G | G70A tRNA minihelix ending in ccacca | rna | 18 | — | — |
| H | RNA (5'-D(P*CP*G)-3') | rna | 2 | — | — |
| I | RNA (5'-D(P*GP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.80 | 0.82 | 59 | empty |
| 2 | 924 | 0.79 | 0.82 | 68 | empty |
| 3 | 777 | 0.78 | 0.82 | 47 | empty |
| 4 | 765 | 0.75 | 0.80 | 46 | empty |
| 5 | 577 | 0.74 | 0.82 | 60 | GOL |
Interfaces
14 interfaces between chains.
- C–F · 2612 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1151 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 1134 Ų buried · 27 hydrogen bonds · protein-nucleic
- E–F · 1015 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 724 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 4X4T · Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA… · the same entry in another collection · chain G against G, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · 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 O28126
- Elsewhere: RCSB PDB 4X4T · PDBe 4X4T · UniProt O28126
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