MolNFT v1 · #133130 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in complex with Z2856434920
5RMB: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in complex with Z2856434920”. X-ray diffraction, 3 ligands (VWV, ZN, PO4), 11 pockets (best druggability 0.80). MolNFT v1 #133130 on GenesisL1: 3D…
- PDB
- 5RMB
- 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
- VWV, ZN, PO4
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 572 | 31% helix, 24% strand | P0DTD1 |
| B | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 585 | 29% helix, 24% strand | P0DTD1 |
Ligands and binding sites
- VWV · ethyl (1,1-dioxo-1lambda~6~,4-thiazinan-4-yl)acetate · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.80 | 0.81 | 105 | empty |
| 2 | 762 | 0.77 | 0.81 | 84 | empty |
| 3 | 384 | 0.65 | 0.79 | 45 | empty |
| 4 | 202 | 0.57 | 0.81 | 28 | PO4 |
| 5 | 168 | 0.56 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5RMB · PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex… · 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 P0DTD1
- Elsewhere: RCSB PDB 5RMB · PDBe 5RMB · UniProt P0DTD1
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