MolNFT v1 · #133134 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in complex with Z54226006
5RMF: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in complex with Z54226006”. X-ray diffraction, 3 ligands (NX7, ZN, PO4), 13 pockets (best druggability 0.75). MolNFT v1 #133134 on GenesisL1: 3D structure…
- PDB
- 5RMF
- 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
- NX7, ZN, PO4
- Pockets
- 13 · best druggability 0.75
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 | 30% helix, 24% strand | P0DTD1 |
| B | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 585 | 30% helix, 24% strand | P0DTD1 |
Ligands and binding sites
- NX7 · (2,6-difluorophenyl)(pyrrolidin-1-yl)methanone · 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
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.75 | 0.84 | 50 | empty |
| 2 | 227 | 0.69 | 0.86 | 33 | empty |
| 3 | 275 | 0.64 | 0.81 | 35 | empty |
| 4 | 177 | 0.61 | 0.83 | 27 | PO4 |
| 5 | 333 | 0.58 | 0.76 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5RMF · 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 5RMF · PDBe 5RMF · UniProt P0DTD1
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