Research workbench
Structure of replicating SARS-cov-2 polymerase
Analyse Structure of replicating SARS-cov-2 polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YYT
- Type
- protein + RNA
- Length
- 1,352 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP12; NSP8; NSP7; RNA product
- 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
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NSP12 (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 | 853 | 46% helix, 14% strand | P0DTD1 |
| B, D | NSP8 (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 | 186 | 58% helix, 16% strand | P0DTD1 |
| C | NSP7 (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 | 73 | 79% helix, 0% strand | P0DTD1 |
| P, Q, U | RNA product | rna | 14 | — | — |
| T | RNA product | rna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.81 | 0.97 | 24 | empty |
| 2 | 1184 | 0.79 | 0.81 | 87 | empty |
| 3 | 471 | 0.74 | 0.83 | 39 | empty |
| 4 | 407 | 0.67 | 0.80 | 52 | empty |
| 5 | 685 | 0.65 | 0.76 | 40 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2567 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1396 Ų buried · 4 hydrogen bonds · protein-protein
- A–T · 1088 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 831 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 819 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6YYT · Structure of replicating SARS-CoV-2 polymerase · 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 6YYT · PDBe 6YYT · UniProt P0DTD1
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