MolNFT v1 · #186444 · protein + RNA
SARS-cov-2 replication-transcription complex bound to NSP13 helicase - NSP13(1)-rtc
7RE2 · RNA-directed RNA polymerase: “SARS-cov-2 replication-transcription complex bound to NSP13 helicase - NSP13(1)-rtc”. Electron microscopy, 5 ligands (1N7, ADP, AF3), 20 pockets (best druggability 0.79). MolNFT v1 #186444 on GenesisL1…
- PDB
- 7RE2
- Type
- protein + RNA
- Length
- 2,034 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7…
- EC
- 2.7.7.48, 3.6.4.12, 3.6.4.13
- UniProt
- P0DTD1
- Ligands
- 1N7, ADP, AF3, ZN, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 7 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 42% helix, 16% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 186 | 63% helix, 16% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 75 | 76% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 185 | 58% helix, 17% strand | P0DTD1 |
| E | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 590 | 27% helix, 20% strand | P0DTD1 |
| P | Product RNA | rna | 34 | — | — |
| T | Template RNA | rna | 37 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 3 copies · chains A, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, E
- AF3 · Aluminum fluoride · ligand · chains E
- ZN · Zinc ion · metal · 5 copies · chains A, E
- MG · Magnesium ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.79 | 0.81 | 80 | empty |
| 2 | 731 | 0.77 | 0.82 | 82 | empty |
| 3 | 111 | 0.76 | 0.96 | 22 | empty |
| 4 | 552 | 0.72 | 0.80 | 36 | empty |
| 5 | 778 | 0.69 | 0.76 | 62 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2636 Ų buried · 16 hydrogen bonds · protein-protein
- P–T · 1566 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- C–D · 1508 Ų buried · 5 hydrogen bonds · protein-protein
- A–T · 1110 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 924 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7RE2 · SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(1)-RTC · 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 7RE2 · PDBe 7RE2 · UniProt P0DTD1
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