MolNFT v1 · #74392 · protein + RNA
How the cca-adding enzyme selects adenine over cytosine in position 76 of tRNA
3OVB: “How the cca-adding enzyme selects adenine over cytosine in position 76 of tRNA”. X-ray diffraction, 4 ligands (ATP, POP, MG), 10 pockets (best druggability 0.74). MolNFT v1 #74392 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3OVB
- Type
- protein + RNA
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; RNA (35-mer)
- EC
- 2.7.7.25, 2.7.7.21
- UniProt
- O28126
- Ligands
- ATP, POP, MG, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21) | protein | 441 | 44% helix, 22% strand | O28126 |
| B | Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21) | protein | 437 | 43% helix, 22% strand | O28126 |
| C, D | RNA (35-mer) | rna | 35 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B, D
- POP · Pyrophosphate 2- · ligand · 2 copies · chains B, D, A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.74 | 0.77 | 89 | empty |
| 2 | 1081 | 0.74 | 0.77 | 79 | EDO |
| 3 | 396 | 0.63 | 0.78 | 34 | MG, POP |
| 4 | 317 | 0.61 | 0.79 | 36 | POP, MG |
| 5 | 456 | 0.57 | 0.74 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2522 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1568 Ų buried · 49 hydrogen bonds · protein-nucleic
- A–C · 1562 Ų buried · 40 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3OVB · How the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA · the same entry in another collection · chain D against D, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain B 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 3OVB · PDBe 3OVB · UniProt O28126
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