Research workbench
Structure of COVID-19 RNA-dependent RNA polymerase bound to suramin
Analyse Structure of COVID-19 RNA-dependent RNA polymerase bound to suramin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D4F
- Type
- protein
- Length
- 1,181 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 8; Non-structural protein 7; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- H3U, ZN
- Pockets
- 12 · best druggability 0.69
Structure
electron microscopy · 4 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Non-structural protein 8 | protein | 114 | 35% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 63 | 78% helix, 0% strand | P0DTD1 |
| G | Non-structural protein 8 | protein | 106 | 30% helix, 28% strand | P0DTD1 |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 898 | 43% helix, 18% strand | P0DTD1 |
Ligands and binding sites
- H3U · 8-(3-(3-aminobenzamido)-4-methylbenzamido)naphthalene-1,3,5-trisulfonic acid · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.69 | 0.79 | 70 | empty |
| 2 | 261 | 0.59 | 0.79 | 38 | empty |
| 3 | 434 | 0.56 | 0.74 | 49 | empty |
| 4 | 169 | 0.49 | 0.77 | 31 | empty |
| 5 | 97 | 0.47 | 0.81 | 17 | H3U |
Interfaces
5 interfaces between chains.
- B–A · 2542 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 1087 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 799 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 5 hydrogen bonds · protein-protein
- G–A · 155 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7D4F · Structure of COVID-19 RNA-dependent RNA polymerase bound to suramin · 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 7D4F · PDBe 7D4F · UniProt P0DTD1
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