MolNFT v1 · #153570 · protein + RNA
Viral helicase protein
6JIM: “Viral helicase protein”. X-ray diffraction, 5 ligands (ADP, MG, AL), 13 pockets (best druggability 0.78). MolNFT v1 #153570 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JIM
- Type
- protein + RNA
- Length
- 923 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helicase; RNA (5'-R(P*UP*UP*UP*UP*UP)-3')
- Ligands
- ADP, MG, AL, F, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helicase | protein | 454 | 38% helix, 21% strand | — |
| B | Helicase | protein | 455 | 38% helix, 21% strand | — |
| C, D | RNA (5'-R(P*UP*UP*UP*UP*UP)-3') | rna | 7 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- AL · Aluminum ion · metal · 2 copies · chains A, B
- F · Fluoride ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.78 | 0.86 | 49 | GOL |
| 2 | 641 | 0.77 | 0.83 | 52 | GOL |
| 3 | 124 | 0.48 | 0.80 | 25 | ADP, MG, AL, F |
| 4 | 179 | 0.47 | 0.76 | 33 | GOL |
| 5 | 112 | 0.46 | 0.80 | 25 | ADP, MG, AL, F |
Interfaces
3 interfaces between chains.
- A–C · 1142 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 1125 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 390 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6JIM · Viral helicase protein · 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
- Elsewhere: RCSB PDB 6JIM · PDBe 6JIM
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