Research workbench
In situ structure of bmcpv RNA dependent RNA polymerase at initiation state
Analyse In situ structure of bmcpv RNA dependent RNA polymerase at initiation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TY9
- Type
- protein + RNA
- Length
- 1,747 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; Viral structural protein 4; Transcript; Non-template RNA…
- UniProt
- Q993A4, Q9IR43
- Ligands
- GTP, GTA, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 1208 | 45% helix, 12% strand | Q993A4 |
| B | Viral structural protein 4 | protein | 501 | 40% helix, 14% strand | Q9IR43 |
| M | Transcript | rna | 1 | — | — |
| N | Non-template RNA (5'-D(*(GTA))- R(P*GP*UP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 18 | — | — |
| T | Template RNA (5'- R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*AP*CP*U)-3') | rna | 19 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, M, T
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A, N
- MG · Magnesium ion · metal · 3 copies · chains A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.83 | 0.86 | 64 | empty |
| 2 | 858 | 0.82 | 0.84 | 88 | GTP, MG |
| 3 | 795 | 0.80 | 0.84 | 99 | GTA |
| 4 | 149 | 0.78 | 0.95 | 33 | empty |
| 5 | 183 | 0.77 | 0.92 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3626 Ų buried · 53 hydrogen bonds · protein-protein
- N–T · 663 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–T · 573 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–N · 439 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–M · 191 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6TY9 · In situ structure of BmCPV RNA dependent RNA polymerase at initiation state · the same entry in another collection · chain B against B, 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 6TY9 · PDBe 6TY9 · UniProt Q993A4 · UniProt Q9IR43
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