MolNFT v1 · #167724 · protein
Naegleria gruberi RNA ligase with ppi
6VTF: “Naegleria gruberi RNA ligase with ppi”. X-ray diffraction, 1 ligand (POP), 14 pockets (best druggability 0.79). MolNFT v1 #167724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VTF
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA ligase
- UniProt
- D2W2Z5
- Ligands
- POP
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA ligase | protein | 337 | 19% helix, 37% strand | D2W2Z5 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.79 | 0.81 | 76 | POP |
| 2 | 1038 | 0.77 | 0.79 | 87 | POP |
| 3 | 761 | 0.77 | 0.82 | 65 | POP |
| 4 | 732 | 0.75 | 0.80 | 73 | POP |
| 5 | 835 | 0.73 | 0.78 | 80 | empty |
Interfaces
5 interfaces between chains.
- B–C · 507 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 431 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 414 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6VTF · Naegleria gruberi RNA ligase with PPi · 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 6VTF · PDBe 6VTF · UniProt D2W2Z5
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