Research workbench
Naegleria gruberi RNA ligase K170A mutant with ATP and mn
Analyse Naegleria gruberi RNA ligase K170A mutant with ATP and mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VT6
- Type
- protein
- Length
- 335 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA ligase
- UniProt
- D2W2Z5
- Ligands
- ATP, MN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA ligase | protein | 335 | 20% helix, 35% strand | D2W2Z5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.78 | 0.83 | 57 | ATP, MN |
| 2 | 189 | 0.52 | 0.78 | 22 | empty |
| 3 | 58 | 0.28 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VT6 · Naegleria gruberi RNA ligase K170A mutant with ATP and 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 6VT6 · PDBe 6VT6 · UniProt D2W2Z5
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