Research workbench
Crystal structure of SARS-cov-2 (COVID-19) NSP3 macrodomain in complex with hepes
Analyse Crystal structure of SARS-cov-2 (COVID-19) NSP3 macrodomain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YWK
- Type
- protein
- Length
- 861 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP3 macrodomain
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | NSP3 macrodomain (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 172 | 41% helix, 19% strand | P0DTD1 |
| C | NSP3 macrodomain (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 173 | 42% helix, 18% strand | P0DTD1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, E
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, D, B, C, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.76 | 0.79 | 103 | EPE, EDO |
| 2 | 456 | 0.71 | 0.81 | 48 | empty |
| 3 | 363 | 0.65 | 0.79 | 41 | EDO |
| 4 | 449 | 0.64 | 0.77 | 45 | EDO |
| 5 | 207 | 0.55 | 0.78 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–D · 534 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 478 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 308 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 123 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YWK · Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES · 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 6YWK · PDBe 6YWK · UniProt P0DTD1
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