Research workbench
SARS-cov-2 macrodomain in complex with ADP-hpm
Analyse SARS-cov-2 macrodomain in complex with ADP-hpm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z72
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB
- 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
- A3R, MLT, NA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB (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 | 174 | 41% helix, 17% strand | P0DTD1 |
| B, C | Replicase polyprotein 1AB (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 |
| D | Replicase polyprotein 1AB (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, 17% strand | P0DTD1 |
Ligands and binding sites
- A3R · Adenosine Diphosphate (Hydroxymethyl)pyrrolidine monoalcohol · ligand · 4 copies · chains A, B, C, D
- MLT · D-malate · ligand · chains D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.66 | 0.79 | 40 | A3R |
| 2 | 420 | 0.65 | 0.78 | 42 | A3R |
| 3 | 204 | 0.59 | 0.80 | 32 | A3R |
| 4 | 195 | 0.57 | 0.80 | 32 | A3R |
Interfaces
2 interfaces between chains.
- C–D · 283 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Z72 · SARS-CoV-2 Macrodomain in complex with ADP-HPM · 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 6Z72 · PDBe 6Z72 · UniProt P0DTD1
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