Research workbench
Archaeal ATP-dependent RNA ligase - form 1
Analyse Archaeal ATP-dependent RNA ligase - form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D1O
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA ligase
- UniProt
- O27289
- Ligands
- ATP, MG, SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA ligase | protein | 375 | 37% helix, 26% strand | O27289 |
| B | ATP-dependent RNA ligase | protein | 375 | 38% helix, 26% strand | O27289 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 5 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 | 611 | 0.70 | 0.78 | 55 | ATP |
| 2 | 505 | 0.60 | 0.74 | 44 | SO4, MG |
| 3 | 125 | 0.53 | 0.82 | 16 | empty |
| 4 | 93 | 0.51 | 0.83 | 15 | empty |
| 5 | 57 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2324 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5D1O · Archaeal ATP-dependent RNA ligase - form 1 · the same entry in another collection · chain A against A, TM-score 1.00
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 O27289
- Elsewhere: RCSB PDB 5D1O · PDBe 5D1O · UniProt O27289
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