Research workbench
The NSP12-NSP7-NSP8 complex bound to the template-primer RNA and triphosphate form of REMDESIVIR(RTP)
Analyse The NSP12-NSP7-NSP8 complex bound to the template-primer RNA and triphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BV2
- Type
- protein + RNA
- Length
- 1,036 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7; Primer…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- POP, F86, ZN, MG
- Pockets
- 13 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 834 | 46% helix, 16% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 39% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 63 | 84% helix, 0% strand | P0DTD1 |
| P | Primer | rna | 11 | — | — |
| T | Templete | rna | 14 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A
- F86 · [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-F][1, 2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, P, T
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.80 | 0.96 | 27 | empty |
| 2 | 1044 | 0.80 | 0.82 | 78 | POP, MG, F86 |
| 3 | 396 | 0.66 | 0.79 | 41 | empty |
| 4 | 60 | 0.55 | 0.88 | 18 | empty |
| 5 | 196 | 0.54 | 0.79 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2527 Ų buried · 12 hydrogen bonds · protein-protein
- A–T · 1028 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 800 Ų buried · 6 hydrogen bonds · protein-protein
- A–P · 626 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 499 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7BV2 · The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of… · 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 7BV2 · PDBe 7BV2 · UniProt P0DTD1
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