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Pandda analysis group deposition -- crystal structure of SARS-cov-2 helicase in complex with Z85956652
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
- 5RML
- 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
- VXD, ZN, PO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 585 | 28% helix, 24% strand | P0DTD1 |
| A | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 572 | 30% helix, 23% strand | P0DTD1 |
Ligands and binding sites
- VXD · N-(3-chloro-2-methylphenyl)glycinamide · ligand · chains A
- 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
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.75 | 0.82 | 44 | VXD |
| 2 | 274 | 0.71 | 0.85 | 41 | empty |
| 3 | 472 | 0.67 | 0.79 | 54 | empty |
| 4 | 295 | 0.65 | 0.81 | 39 | empty |
| 5 | 194 | 0.62 | 0.83 | 28 | PO4 |
Interfaces
1 interface between chains.
- B–A · 661 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5RML · 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 5RML · PDBe 5RML · UniProt P0DTD1
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