Research workbench
Complex structure of cca-adding enzyme, mini-dcc and CTP
Analyse Complex structure of cca-adding enzyme, mini-dcc and CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DVI
- Type
- protein + RNA
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (34-mer); Cca-adding enzyme
- EC
- 2.7.7.25, 2.7.7.21
- UniProt
- O28126
- Ligands
- CTP, MG, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA (34-mer) | rna | 34 | — | — |
| A | Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21) | protein | 431 | 45% helix, 20% strand | O28126 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains B, A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.74 | 0.83 | 51 | MG, CTP |
| 2 | 471 | 0.58 | 0.74 | 46 | empty |
| 3 | 439 | 0.54 | 0.73 | 30 | SO4 |
| 4 | 347 | 0.53 | 0.74 | 25 | empty |
| 5 | 153 | 0.45 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 1480 Ų buried · 33 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 2DVI · PDBe 2DVI · UniProt O28126
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