MolNFT v1 · #167717 · protein
Naegleria gruberi RNA ligase E312A mutant with AMP and mn
6VT8: “Naegleria gruberi RNA ligase E312A mutant with AMP and mn”. X-ray diffraction, 2 ligands (AMP, MN), 2 pockets (best druggability 0.79). MolNFT v1 #167717 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VT8
- Type
- protein
- Length
- 336 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA ligase
- UniProt
- D2W2Z5
- Ligands
- AMP, MN
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA ligase | protein | 336 | 20% helix, 35% strand | D2W2Z5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.79 | 0.85 | 62 | AMP, MN |
| 2 | 232 | 0.57 | 0.78 | 22 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VT8 · Naegleria gruberi RNA ligase E312A mutant with AMP 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 6VT8 · PDBe 6VT8 · UniProt D2W2Z5
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