Research workbench
Crystal structure of SARS-cov-2 (COVID-19) NSP3 macrodomain in complex with mes
Analyse Crystal structure of SARS-cov-2 (COVID-19) NSP3 macrodomain in complex with mes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YWM
- Type
- protein
- Length
- 512 residues
- Chains
- 3
- 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 0.68
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 | 40% helix, 20% strand | P0DTD1 |
| B | 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 | 171 | 40% 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 | 169 | 39% helix, 20% strand | P0DTD1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.68 | 0.81 | 49 | MES |
| 2 | 428 | 0.66 | 0.79 | 33 | EDO |
| 3 | 185 | 0.58 | 0.81 | 29 | EDO |
| 4 | 215 | 0.57 | 0.79 | 32 | MES, EDO |
| 5 | 83 | 0.48 | 0.82 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 547 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 359 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6YWM · Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with MES · 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 6YWM · PDBe 6YWM · UniProt P0DTD1
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