Research workbench
SARS-cov-2 replication-transcription complex bound to NSP13 helicase - NSP13(2)-rtc - apo class
Analyse SARS-cov-2 replication-transcription complex bound to NSP13 helicase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RDZ
- Type
- protein + RNA
- Length
- 2,622 residues
- Chains
- 8
- 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
- ADP, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 43% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 186 | 62% helix, 16% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 73 | 78% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 185 | 57% helix, 16% strand | P0DTD1 |
| E, F | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 590 | 28% helix, 20% strand | P0DTD1 |
| P | Product RNA | rna | 34 | — | — |
| T | Template RNA | rna | 37 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ZN · Zinc ion · metal · 8 copies · chains A, E, F
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.82 | 0.84 | 107 | empty |
| 2 | 1062 | 0.81 | 0.83 | 113 | empty |
| 3 | 755 | 0.80 | 0.84 | 61 | empty |
| 4 | 120 | 0.77 | 0.96 | 22 | empty |
| 5 | 538 | 0.72 | 0.80 | 41 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2659 Ų buried · 14 hydrogen bonds · protein-protein
- P–T · 1578 Ų buried · 116 hydrogen bonds · nucleic-nucleic
- C–D · 1401 Ų buried · 3 hydrogen bonds · protein-protein
- A–T · 1139 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 938 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7RDZ · SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - apo… · 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 7RDZ · PDBe 7RDZ · UniProt P0DTD1
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