MolNFT v1 · #171481 · protein
SARS-cov-2 macrodomain in complex with ADP-hpd
6Z6I · Replicase polyprotein 1AB: “SARS-cov-2 macrodomain in complex with ADP-hpd”. X-ray diffraction, 2 ligands (A1R, NA), 4 pockets (best druggability 0.67). MolNFT v1 #171481 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z6I
- 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
- A1R, NA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 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 | 172 | 41% helix, 17% strand | P0DTD1 |
| B | 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 | 40% helix, 17% strand | P0DTD1 |
| 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 | 174 | 41% helix, 20% 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 | 173 | 41% helix, 18% strand | P0DTD1 |
Ligands and binding sites
- A1R · 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-dihydroxypyrrolidin-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]adenosine · ligand · 6 copies · chains A, B, C, D
- NA · Sodium ion · metal · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A, B
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 | 495 | 0.67 | 0.78 | 54 | A1R, EDO |
| 2 | 402 | 0.65 | 0.79 | 50 | A1R, MPO |
| 3 | 212 | 0.61 | 0.81 | 32 | A1R |
| 4 | 211 | 0.61 | 0.81 | 33 | A1R |
Interfaces
2 interfaces between chains.
- A–B · 280 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 258 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6Z6I · SARS-CoV-2 Macrodomain in complex with ADP-HPD · 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 6Z6I · PDBe 6Z6I · UniProt P0DTD1
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