Research workbench
In situ structure of bmcpv RNA-dependent RNA polymerase at early- elongation state
Analyse In situ structure of bmcpv RNA-dependent RNA polymerase at early- elongation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TZ1
- Type
- protein + RNA
- Length
- 1,732 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; Viral structural protein 4; Transcript…
- EC
- 2.7.7.48
- UniProt
- Q993A4, Q9IR43
- Ligands
- GTA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 1208 | 45% helix, 11% strand | Q993A4 |
| B | Viral structural protein 4 | protein | 501 | 39% helix, 14% strand | Q9IR43 |
| M | Transcript (5'-R(P*UP*UP*UP*UP*UP*CP*CP*CP*U)-3') | rna | 9 | — | — |
| N | Non-template RNA (5'-D(*(GTA))-R(P*GP*UP*A)-3') | rna | 3 | — | — |
| T | Template RNA (5'-R(P*AP*GP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 11 | — | — |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A, N
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 | 592 | 0.85 | 0.90 | 84 | empty |
| 2 | 1064 | 0.84 | 0.85 | 90 | empty |
| 3 | 999 | 0.83 | 0.84 | 83 | empty |
| 4 | 142 | 0.79 | 0.96 | 28 | empty |
| 5 | 90 | 0.75 | 0.97 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3814 Ų buried · 39 hydrogen bonds · protein-protein
- A–T · 1062 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–M · 866 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–N · 394 Ų buried · 7 hydrogen bonds · protein-nucleic
- M–T · 381 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6TZ1 · In situ structure of BmCPV RNA-dependent RNA polymerase at early-elongation state · 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 Q993A4
- Every structure of UniProt Q9IR43
- Elsewhere: RCSB PDB 6TZ1 · PDBe 6TZ1 · UniProt Q993A4 · UniProt Q9IR43
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