Research workbench
RdRp complex
Analyse RdRp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K32
- Type
- protein + RNA
- Length
- 7,730 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Cypovirus 1
- Molecule
- RNA-dependent RNA polymerase; Viral structural protein 4; RNA (5'-R(P*UP*UP*AP*CP*U)-3')…
- UniProt
- D0EZK6, C7EWL9, D3JWE6
- Ligands
- MG7, DPO, A2M, UTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.2 · 8 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 1208 | 42% helix, 9% strand | D0EZK6 |
| B | Viral structural protein 4 | protein | 498 | 37% helix, 9% strand | C7EWL9 |
| t | RNA (5'-R(P*UP*UP*AP*CP*U)-3') | rna | 5 | — | — |
| p | RNA (5'-D(*(3PO))-R(*AP*G)-3' | rna | 2 | — | — |
| C | VP1 | protein | 1220 | 31% helix, 15% strand | D3JWE6 |
| D | VP1 | protein | 1197 | 30% helix, 17% strand | D3JWE6 |
| E, F | VP1 | protein | 1191 | 31% helix, 15% strand | D3JWE6 |
| G | VP1 | protein | 1218 | 30% helix, 16% strand | D3JWE6 |
Ligands and binding sites
- MG7 · 7-methylguanosine · ligand · chains A
- DPO · Diphosphate · ligand · chains A
- A2M · 2'-O-methyladenosine 5'-(dihydrogen phosphate) · ligand · chains A
- UTP · Uridine 5'-triphosphate · ligand · chains A, t, p
- 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
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.89 | 0.91 | 115 | empty |
| 2 | 431 | 0.85 | 0.92 | 59 | empty |
| 3 | 1071 | 0.82 | 0.83 | 108 | empty |
| 4 | 373 | 0.81 | 0.90 | 64 | empty |
| 5 | 881 | 0.78 | 0.81 | 82 | MG, UTP |
Interfaces
16 interfaces between chains.
- A–B · 3786 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 2148 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2024 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1413 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 1095 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6K32 · Rdrp complex · 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 D0EZK6
- Every structure of UniProt C7EWL9
- Every structure of UniProt D3JWE6
- Elsewhere: RCSB PDB 6K32 · PDBe 6K32 · UniProt D0EZK6 · UniProt C7EWL9 · UniProt D3JWE6
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