MolNFT v1 · #109506 · protein + RNA
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in ccac and CTP
4X4Q: “Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in…”. X-ray diffraction, 2 ligands (CTP, MG), 12 pockets (best druggability 0.75). MolNFT v1 #109506 on GenesisL1: 3D…
- PDB
- 4X4Q
- Type
- protein + RNA
- Length
- 946 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; G70A tRNA minihelix ending in ccac
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- CTP, MG
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.72) | protein | 443 | 42% helix, 21% strand | O28126 |
| B | G70A tRNA minihelix ending in ccac | rna | 36 | — | — |
| C | Cca-adding enzyme (EC 2.7.7.72) | protein | 437 | 44% helix, 20% strand | O28126 |
| D | G70A tRNA minihelix ending in ccac | rna | 30 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.75 | 0.82 | 47 | MG, CTP |
| 2 | 940 | 0.74 | 0.78 | 63 | empty |
| 3 | 1049 | 0.74 | 0.77 | 72 | empty |
| 4 | 532 | 0.74 | 0.82 | 50 | CTP, MG |
| 5 | 558 | 0.62 | 0.75 | 34 | PEG |
Interfaces
3 interfaces between chains.
- A–C · 2626 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1418 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 1345 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 4X4Q · 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 0.97
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 4X4Q · PDBe 4X4Q · UniProt O28126
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