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Mechanism of cca-adding enzymes specificity revealed by crystal structures of ternary complexes
Analyse Mechanism of cca-adding enzymes specificity revealed by crystal structures of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SZ1
- Type
- protein + RNA
- Length
- 1,026 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-RNA (76-mer); TRNA nucleotidyltransferase
- EC
- 2.7.7.25
- UniProt
- O28126
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | T-RNA (76-mer) | rna | 76 | — | — |
| A, B | TRNA nucleotidyltransferase (EC 2.7.7.25) | protein | 437 | 41% helix, 21% strand | O28126 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.80 | 0.87 | 52 | empty |
| 2 | 521 | 0.79 | 0.86 | 53 | empty |
| 3 | 1011 | 0.75 | 0.78 | 71 | empty |
| 4 | 924 | 0.74 | 0.78 | 64 | empty |
| 5 | 952 | 0.70 | 0.76 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2507 Ų buried · 21 hydrogen bonds · protein-protein
- F–B · 1534 Ų buried · 50 hydrogen bonds · protein-nucleic
- E–A · 1518 Ų buried · 39 hydrogen bonds · protein-nucleic
- E–F · 28 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 28 modified (nucleotide modification).
Compared structures
- 1SZ1 · Mechanism of CCA-adding enzymes specificity revealed by crystal structures of ternary… · the same entry in another collection · chain E against E, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 1SZ1 · PDBe 1SZ1 · UniProt O28126
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