MolNFT v2 · #184421 · protein
Crystal structure from SARS-CoV-2 NendoU NSP15
7KEH · Uridylate-specific endoribonuclease: “Crystal structure from SARS-CoV-2 NendoU NSP15”. X-ray diffraction at 2.59, 1 ligand (SO4), 7 pockets (best druggability 0.58). MolNFT v2 #184421 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7KEH
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.59
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · resolution 2.59 · 1 distinct chain · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 22% helix, 32% strand | P0DTD1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · 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 | 166 | 0.58 | 0.82 | 23 | empty |
| 2 | 190 | 0.58 | 0.81 | 26 | empty |
| 3 | 105 | 0.35 | 0.73 | 18 | empty |
| 4 | 62 | 0.32 | 0.76 | 15 | empty |
| 5 | 72 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 602 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7KEH · Crystal structure from SARS-cov-2 nendou NSP15 · 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 7KEH · PDBe 7KEH · UniProt P0DTD1
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