Research workbench
Structure of elongating SARS-cov-2 RNA-dependent RNA polymerase with AMP at position -4 (structure 3)
Analyse Structure of elongating SARS-cov-2 RNA-dependent RNA polymerase with AMP at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B3D
- Type
- protein + RNA
- Length
- 1,013 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARS-cov-2 RNA-dependent RNA polymerase NSP12; SARS-cov-2 NSP8; SARS-cov-2 NSP7; 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
- ZN
- 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 | SARS-cov-2 RNA-dependent RNA polymerase 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 | 814 | 46% helix, 16% strand | P0DTD1 |
| B | SARS-cov-2 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 | 115 | 40% helix, 25% strand | P0DTD1 |
| C | SARS-cov-2 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 | 62 | 87% helix, 0% strand | P0DTD1 |
| P | RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3') | rna | 10 | — | — |
| T | RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3') | 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
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 | 1029 | 0.80 | 0.82 | 83 | empty |
| 2 | 136 | 0.79 | 0.97 | 27 | empty |
| 3 | 482 | 0.69 | 0.80 | 64 | empty |
| 4 | 248 | 0.54 | 0.77 | 37 | empty |
| 5 | 137 | 0.52 | 0.80 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2435 Ų buried · 12 hydrogen bonds · protein-protein
- A–T · 1093 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 818 Ų buried · 9 hydrogen bonds · protein-protein
- A–P · 647 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 503 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 7B3D · Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with AMP at position -4… · 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 7B3D · PDBe 7B3D · UniProt P0DTD1
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