Research workbench
Structure and mechanism of a eukaryal nick-sealing RNA ligase K170M+MN
Analyse Structure and mechanism of a eukaryal nick-sealing RNA ligase K170M+MN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5COV
- Type
- protein
- Length
- 339 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naegleria gruberi RNA ligase
- UniProt
- D2W2Z5
- Ligands
- MN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Naegleria gruberi RNA ligase | protein | 339 | 22% helix, 35% strand | D2W2Z5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.80 | 0.86 | 64 | MN |
| 2 | 146 | 0.47 | 0.77 | 22 | empty |
| 3 | 54 | 0.27 | 0.74 | 19 | empty |
Compared structures
- 5COV · Structure and mechanism of a eukaryal nick-sealing RNA ligase K170M+Mn · 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 D2W2Z5
- Elsewhere: RCSB PDB 5COV · PDBe 5COV · UniProt D2W2Z5
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