Research workbench
NSP7-NSP8-NSP12 SARS-COV2 RNA-dependent RNA polymerase in complex with TEMPLATE:PRIMER dsrna and favipiravir-rtp
Analyse NSP7-NSP8-NSP12 SARS-COV2 RNA-dependent RNA polymerase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AAP
- Type
- protein + RNA
- Length
- 1,141 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 12; Non-structural protein 8; Non-structural protein 7; RNA…
- 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
- POP, GE6, MG, ZN
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 12 (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 | 911 | 43% helix, 19% strand | P0DTD1 |
| B | Non-structural protein 8 (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 | 114 | 39% helix, 26% strand | P0DTD1 |
| C | Non-structural protein 7 (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 | 67 | 78% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 (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 | 28 | 86% helix, 0% strand | P0DTD1 |
| P | RNA (5'-R(P*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') | rna | 9 | — | — |
| T | RNA (5'-R(P*UP*UP*CP*AP*UP*AP*AP*CP*UP*UP*AP*A)-3') | rna | 12 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A
- GE6 · [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 3 copies · chains A, P
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.81 | 0.97 | 29 | empty |
| 2 | 1022 | 0.80 | 0.82 | 72 | MG, GE6 |
| 3 | 375 | 0.65 | 0.79 | 40 | empty |
| 4 | 315 | 0.62 | 0.79 | 42 | MG, POP |
| 5 | 89 | 0.58 | 0.87 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2580 Ų buried · 16 hydrogen bonds · protein-protein
- A–T · 1105 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 842 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 805 Ų buried · 0 hydrogen bonds · protein-protein
- A–P · 630 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 7AAP · Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer… · 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 7AAP · PDBe 7AAP · UniProt P0DTD1
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