MolNFT v2 · #227785 · protein
Structure of T4 RNA Ligase 1 bound to ATP and Mg
9DO4: “Structure of T4 RNA Ligase 1 bound to ATP and Mg”. X-ray diffraction at 2.6, 2 ligands (ATP, MG), 6 pockets (best druggability 0.77). MolNFT v2 #227785 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 9DO4
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Enterobacteria phage T4
- Molecule
- RNA ligase 1
- EC
- 6.5.1.3
- UniProt
- P00971
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA ligase 1 (EC 6.5.1.3) | protein | 367 | 42% helix, 22% strand | P00971 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.77 | 0.82 | 68 | MG, ATP |
| 2 | 95 | 0.46 | 0.80 | 16 | empty |
| 3 | 71 | 0.45 | 0.82 | 19 | empty |
| 4 | 115 | 0.40 | 0.75 | 22 | empty |
| 5 | 63 | 0.34 | 0.76 | 12 | empty |
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 P00971
- Elsewhere: RCSB PDB 9DO4 · PDBe 9DO4 · UniProt P00971
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