Research workbench
In situ structures of the segmented genome and RNA polymerase complex inside a dsrna virus
Analyse In situ structures of the segmented genome and RNA polymerase complex inside a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JB7
- Type
- protein + RNA
- Length
- 1,744 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cpv RNA-dependent RNA polymerase; Viral structural protein 4; VP1 csp; RNA…
- EC
- 2.7.7.48
- UniProt
- D0EZK6, Q9IR43, D3JWE6
- Ligands
- GTP, CTP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cpv RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 1198 | 46% helix, 11% strand | D0EZK6 |
| B | Viral structural protein 4 | protein | 498 | 43% helix, 13% strand | Q9IR43 |
| C | VP1 csp | protein | 21 | 48% helix, 0% strand | D3JWE6 |
| t | RNA (5'-R(P*GP*GP*GP*GP*GP*G)-3') | rna | 6 | — | — |
| m | RNA (5'-R(P*CP*CP*CP*CP*C)-3') | rna | 5 | — | — |
| D | VP1 csp | protein | 16 | 81% helix, 0% strand | D3JWE6 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CTP · Cytidine-5'-triphosphate · ligand · chains A, t, m
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.84 | 0.86 | 72 | empty |
| 2 | 213 | 0.82 | 0.96 | 46 | empty |
| 3 | 936 | 0.81 | 0.83 | 92 | empty |
| 4 | 1078 | 0.78 | 0.80 | 94 | CTP |
| 5 | 136 | 0.78 | 0.96 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3764 Ų buried · 32 hydrogen bonds · protein-protein
- A–t · 872 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 840 Ų buried · 11 hydrogen bonds · protein-protein
- A–m · 647 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 592 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3JB7 · In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus · 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 Q9IR43
- Every structure of UniProt D3JWE6
- Elsewhere: RCSB PDB 3JB7 · PDBe 3JB7 · UniProt D0EZK6 · UniProt Q9IR43 · UniProt D3JWE6
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