Research workbench
Structure of the qb replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins
Analyse Structure of the qb replicase, an RNA-dependent RNA polymerase consisting of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MMP
- Type
- protein
- Length
- 2,384 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu 2, elongation factor ts; RNA-directed RNA polymerase beta chain
- EC
- 2.7.7.48
- UniProt
- P0A6P1, P0CE48, P14647
- Ligands
- PXN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Elongation factor tu 2, elongation factor ts | protein | 643 | 36% helix, 30% strand | P0A6P1, P0CE48 |
| G, F | RNA-directed RNA polymerase beta chain (EC 2.7.7.48) | protein | 549 | 46% helix, 17% strand | P14647 |
Ligands and binding sites
- PXN · (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol · ligand · 2 copies · chains A, G, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.76 | 0.79 | 137 | empty |
| 2 | 760 | 0.75 | 0.80 | 99 | empty |
| 3 | 783 | 0.68 | 0.75 | 76 | empty |
| 4 | 463 | 0.65 | 0.78 | 49 | empty |
| 5 | 669 | 0.65 | 0.74 | 66 | empty |
Interfaces
4 interfaces between chains.
- C–F · 2706 Ų buried · 34 hydrogen bonds · protein-protein
- A–G · 2683 Ų buried · 33 hydrogen bonds · protein-protein
- G–F · 934 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3MMP · Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A6P1 · AlphaFold monomer V2.0 prediction for elongation factor ts (P0A6P1) · a predicted model of the same protein · chain C against A, TM-score 0.42
- P0CE48 · AlphaFold monomer V2.0 prediction for elongation factor tu 2 (P0CE48) · a predicted model of the same protein · chain A against A, TM-score 0.32
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 P0A6P1
- Every structure of UniProt P0CE48
- Every structure of UniProt P14647
- Elsewhere: RCSB PDB 3MMP · PDBe 3MMP · UniProt P0A6P1 · UniProt P0CE48 · UniProt P14647
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