MolNFT v1 · #34797 · protein + RNA
Complex structure of cca-adding enzyme with trnaminicca
2DRB · TRNA (35-mer): “Complex structure of cca-adding enzyme with trnaminicca”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.61). MolNFT v1 #34797 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DRB
- Type
- protein + RNA
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (35-mer); Cca-adding enzyme
- EC
- 2.7.7.25, 2.7.7.21
- UniProt
- O28126
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA (35-mer) | rna | 35 | — | — |
| A | Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21) | protein | 437 | 43% helix, 20% strand | O28126 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.61 | 0.79 | 35 | SO4 |
| 2 | 533 | 0.59 | 0.73 | 49 | empty |
| 3 | 459 | 0.56 | 0.73 | 27 | SO4 |
| 4 | 353 | 0.53 | 0.73 | 27 | empty |
| 5 | 123 | 0.45 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 1635 Ų buried · 45 hydrogen bonds · protein-nucleic
Compared structures
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 2DRB · PDBe 2DRB · UniProt O28126
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