Research workbench
Complex structure of afcca with trnaminidu
Analyse Complex structure of afcca with trnaminidu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZH9
- Type
- protein + RNA
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; TRNA (33-mer)
- EC
- 2.7.7.25, 2.7.7.21
- UniProt
- O28126
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21) | protein | 437 | 43% helix, 21% strand | O28126 |
| B | TRNA (33-mer) | rna | 33 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.78 | 0.81 | 59 | SO4 |
| 2 | 521 | 0.57 | 0.73 | 33 | SO4 |
| 3 | 371 | 0.54 | 0.74 | 26 | empty |
| 4 | 338 | 0.51 | 0.73 | 32 | empty |
| 5 | 241 | 0.49 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1251 Ų buried · 30 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 2ZH9 · PDBe 2ZH9 · UniProt O28126
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