MolNFT v1 · #14726 · protein
Crystal structure of bacillus stearothermophilus cca-adding enzyme in complex with CTP
1MIY · TRNA cca-adding enzyme: “Crystal structure of bacillus stearothermophilus cca-adding enzyme in complex with CTP”. X-ray diffraction, 2 ligands (CTP, MG), 5 pockets (best druggability 0.62). MolNFT v1 #14726 on GenesisL1: 3D…
- PDB
- 1MIY
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA cca-adding enzyme
- UniProt
- Q7SIB1
- Ligands
- CTP, MG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA cca-adding enzyme | protein | 395 | 56% helix, 11% strand | Q7SIB1 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.62 | 0.75 | 45 | MG, CTP |
| 2 | 487 | 0.60 | 0.75 | 41 | MG, CTP |
| 3 | 66 | 0.30 | 0.74 | 14 | empty |
| 4 | 73 | 0.29 | 0.73 | 12 | empty |
| 5 | 66 | 0.29 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 502 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1MIY · Crystal structure of Bacillus stearothermophilus CCA-adding enzyme in complex with CTP · the same entry in another collection · chain A against A, TM-score 1.00
- Q7SIB1 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (Q7SIB1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q7SIB1
- Elsewhere: RCSB PDB 1MIY · PDBe 1MIY · UniProt Q7SIB1
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