Research workbench
Thosea asigna virus rdrp domain in complex with RNA and nucleotide umpnpp
Analyse Thosea asigna virus rdrp domain in complex with RNA and nucleotide umpnpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OM7
- Type
- protein + RNA
- Length
- 2,575 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
- UniProt
- Q6A562
- Ligands
- 2KH, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 628 | 46% helix, 15% strand | Q6A562 |
| B | RNA-dependent RNA polymerase | protein | 629 | 46% helix, 15% strand | Q6A562 |
| C | RNA-dependent RNA polymerase | protein | 632 | 46% helix, 15% strand | Q6A562 |
| D | RNA-dependent RNA polymerase | protein | 629 | 46% helix, 15% strand | Q6A562 |
| E, G, L | RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3') | rna | 6 | — | — |
| F, H, I, K | RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3') | rna | 8 | — | — |
| J | RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3') | rna | 7 | — | — |
Ligands and binding sites
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · 2 copies · chains A, E, F, B, G, H
- MN · Manganese (II) ion · metal · chains A, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.82 | 0.84 | 87 | PEG |
| 2 | 892 | 0.82 | 0.85 | 60 | 2KH, MN |
| 3 | 1126 | 0.81 | 0.82 | 97 | empty |
| 4 | 1051 | 0.81 | 0.82 | 79 | 2KH |
| 5 | 128 | 0.79 | 0.97 | 30 | empty |
Interfaces
25 interfaces between chains.
- A–B · 2977 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 2932 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 1062 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 964 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–F · 949 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 7OM7 · Thosea asigna virus RdRP domain in complex with RNA and nucleotide UMPNPP · the same entry in another collection · chain L against L, 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 Q6A562
- Elsewhere: RCSB PDB 7OM7 · PDBe 7OM7 · UniProt Q6A562
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.