MolNFT v1 · #109507 · protein + RNA
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in ccacc and ampcpp
4X4R: “Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in…”. X-ray diffraction, 2 ligands (APC, MG), 14 pockets (best druggability 0.76). MolNFT v1 #109507 on GenesisL1: 3D…
- PDB
- 4X4R
- Type
- protein + RNA
- Length
- 947 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; G70A tRNA minihelix ending in ccacc; RNA (5'-D(*CP*G)-3')
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- APC, MG
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 5 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 | 44% helix, 21% strand | O28126 |
| D | G70A tRNA minihelix ending in ccacc | rna | 30 | — | — |
| H | RNA (5'-D(*CP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.76 | 0.81 | 58 | APC, MG |
| 2 | 614 | 0.75 | 0.82 | 62 | APC, MG |
| 3 | 741 | 0.73 | 0.79 | 48 | empty |
| 4 | 857 | 0.73 | 0.77 | 57 | GOL |
| 5 | 505 | 0.62 | 0.76 | 32 | GOL |
Interfaces
5 interfaces between chains.
- A–C · 2622 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1521 Ų buried · 33 hydrogen bonds · protein-nucleic
- C–D · 1435 Ų buried · 34 hydrogen bonds · protein-nucleic
- C–H · 185 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–H · 129 Ų buried · 9 hydrogen bonds · nucleic-nucleic
Compared structures
- 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 4X4R · PDBe 4X4R · UniProt O28126
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