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Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in ccacc and CTP
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
- 4X4S
- Type
- protein + RNA
- Length
- 945 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; G70A tRNA minihelix ending in ccacc
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- CTP, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.72) | protein | 443 | 43% helix, 22% strand | O28126 |
| B | G70A tRNA minihelix ending in ccacc | rna | 35 | — | — |
| C | Cca-adding enzyme (EC 2.7.7.72) | protein | 437 | 43% helix, 21% strand | O28126 |
| D | G70A tRNA minihelix ending in ccacc | rna | 30 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, C
- TAR · D(-)-tartaric acid · additive · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.76 | 0.85 | 53 | CTP, MG |
| 2 | 1172 | 0.74 | 0.77 | 83 | GOL |
| 3 | 937 | 0.74 | 0.78 | 70 | empty |
| 4 | 557 | 0.73 | 0.82 | 41 | CTP, MG |
| 5 | 554 | 0.63 | 0.75 | 34 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 2623 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1517 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–D · 1462 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 4X4S · Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA… · the same entry in another collection · chain A against A, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain C 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 O28126
- Elsewhere: RCSB PDB 4X4S · PDBe 4X4S · UniProt O28126
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