Research workbench
Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in complex with Z26333434
Analyse Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RME
- Type
- protein
- Length
- 1,157 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helicase
- EC
- 3.6.4.12, 3.6.4.13
- UniProt
- P0DTD1
- Ligands
- RYM, ZN, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 585 | 28% helix, 23% strand | P0DTD1 |
| A | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 572 | 31% helix, 24% strand | P0DTD1 |
Ligands and binding sites
- RYM · 4-(benzimidazol-1-ylmethyl)benzenecarbonitrile · ligand · chains B
- ZN · Zinc ion · metal · 6 copies · chains B, A
- PO4 · Phosphate ion · ion · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.78 | 0.81 | 88 | empty |
| 2 | 873 | 0.78 | 0.81 | 92 | empty |
| 3 | 416 | 0.66 | 0.79 | 44 | empty |
| 4 | 155 | 0.61 | 0.84 | 24 | PO4 |
| 5 | 183 | 0.58 | 0.82 | 28 | PO4 |
Interfaces
1 interface between chains.
- B–A · 730 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5RME · PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex… · the same entry in another collection · chain B against B, 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 P0DTD1
- Elsewhere: RCSB PDB 5RME · PDBe 5RME · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.