Research workbench
Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex with EN300-321461
Analyse Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SAF
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- WOY
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 22% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- WOY · 6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidine · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.59 | 0.80 | 29 | empty |
| 2 | 215 | 0.58 | 0.80 | 26 | empty |
| 3 | 141 | 0.43 | 0.75 | 21 | empty |
| 4 | 59 | 0.31 | 0.76 | 14 | empty |
| 5 | 71 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 597 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5SAF · PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU 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 5SAF · PDBe 5SAF · UniProt P0DTD1
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