MolNFT v1 · #167720 · protein
Naegleria gruberi RNA ligase K326A mutant with ATP and mn
6VTB: “Naegleria gruberi RNA ligase K326A mutant with ATP and mn”. X-ray diffraction, 2 ligands (ATP, MN), 4 pockets (best druggability 0.84). MolNFT v1 #167720 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VTB
- Type
- protein
- Length
- 340 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA ligase
- UniProt
- D2W2Z5
- Ligands
- ATP, MN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA ligase | protein | 340 | 19% helix, 36% 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.84 | 0.88 | 62 | ATP, MN |
| 2 | 167 | 0.49 | 0.77 | 23 | empty |
| 3 | 96 | 0.40 | 0.77 | 21 | empty |
| 4 | 76 | 0.33 | 0.75 | 14 | empty |
Compared structures
- 6VTB · Naegleria gruberi RNA ligase K326A 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 6VTB · PDBe 6VTB · UniProt D2W2Z5
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