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Crystal structure of SARS-cov-2 (COVID-19) NSP3 macrodomain in complex with ADP-ribose
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
- 6YWL
- Type
- protein
- Length
- 857 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
- APR, MG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, 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 | 38% helix, 20% 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 | 39% helix, 20% strand | P0DTD1 |
| D | 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 | 168 | 39% helix, 21% strand | P0DTD1 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 2 copies · chains C, E
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, D, B, E, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.78 | 0.80 | 120 | APR, EDO |
| 2 | 560 | 0.70 | 0.79 | 44 | EDO |
| 3 | 403 | 0.69 | 0.81 | 43 | APR, EDO |
| 4 | 380 | 0.62 | 0.77 | 30 | EDO |
| 5 | 222 | 0.59 | 0.80 | 31 | APR |
Interfaces
6 interfaces between chains.
- A–D · 535 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 487 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 397 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 306 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6YWL · Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose · the same entry in another collection · chain E against E, 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 6YWL · PDBe 6YWL · UniProt P0DTD1
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