Research workbench
Crystal structure of SARS-cov-2 macrodomain in complex with ADP- ribose-phosphate (ADP-ribose-2'-phosphate, adprp)
Analyse Crystal structure of SARS-cov-2 macrodomain in complex with ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BF5
- Type
- protein
- Length
- 858 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
- A2R, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 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 | 171 | 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 | 170 | 40% helix, 20% strand | P0DTD1 |
| C, 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 | 172 | 39% helix, 20% strand | P0DTD1 |
| 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 | 173 | 42% helix, 18% strand | P0DTD1 |
Ligands and binding sites
- A2R · [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 4 copies · chains A, E, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, E, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.80 | 0.81 | 131 | A2R, EDO |
| 2 | 351 | 0.68 | 0.81 | 38 | MG, A2R |
| 3 | 383 | 0.63 | 0.78 | 37 | empty |
| 4 | 224 | 0.58 | 0.79 | 32 | A2R |
| 5 | 201 | 0.57 | 0.79 | 32 | A2R |
Interfaces
6 interfaces between chains.
- A–B · 532 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 371 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 286 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 113 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7BF5 · Crystal structure of SARS-CoV-2 macrodomain in complex with ADP-ribose-phosphate… · 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 7BF5 · PDBe 7BF5 · UniProt P0DTD1
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