MolNFT v1 · #179756 · protein
Crystal structure from SARS-cov-2 nendou NSP15
7KF4 · Uridylate-specific endoribonuclease: “Crystal structure from SARS-cov-2 nendou NSP15”. X-ray diffraction, 20 pockets (best druggability 0.87). MolNFT v1 #179756 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KF4
- Type
- protein
- Length
- 2,088 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 23% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.87 | 0.89 | 118 | empty |
| 2 | 267 | 0.76 | 0.89 | 46 | empty |
| 3 | 198 | 0.74 | 0.89 | 45 | empty |
| 4 | 456 | 0.69 | 0.80 | 52 | empty |
| 5 | 411 | 0.68 | 0.80 | 53 | empty |
Interfaces
11 interfaces between chains.
- B–F · 1234 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1221 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1215 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1200 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 1198 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7KF4 · 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 7KF4 · PDBe 7KF4 · UniProt P0DTD1
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