MolNFT v1 · #165524 · protein + RNA
In situ structure of bmcpv RNA dependent RNA polymerase at initiation state
6TY9 · RNA-dependent RNA polymerase: “In situ structure of bmcpv RNA dependent RNA polymerase at initiation state”. Electron microscopy, 3 ligands (GTP, GTA, MG), 20 pockets (best druggability 0.83). MolNFT v1 #165524 on GenesisL1: 3D…
- 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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