Research workbench
In situ structure of bmcpv RNA-dependent RNA polymerase at elongation state
Analyse In situ structure of bmcpv RNA-dependent RNA polymerase at elongation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TZ2
- Type
- protein + RNA
- Length
- 1,799 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; Viral structural protein 4; Transcript RNA (5'…
- EC
- 2.7.7.48
- UniProt
- Q993A4, Q9IR43
- Ligands
- ATP, UTP, MG
- Pockets
- 20 · best druggability 0.84
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 | 43% helix, 12% strand | Q993A4 |
| B | Viral structural protein 4 | protein | 501 | 41% helix, 13% strand | Q9IR43 |
| M | Transcript RNA (5'- R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 18 | — | — |
| N | Non-template RNA (36-mer) | rna | 36 | — | — |
| T | Template RNA (36-mer) | rna | 36 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, N
- UTP · Uridine 5'-triphosphate · ligand · chains A, M, T
- MG · Magnesium ion · metal · 2 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.84 | 0.85 | 99 | UTP, MG |
| 2 | 1087 | 0.82 | 0.83 | 92 | empty |
| 3 | 696 | 0.82 | 0.86 | 79 | empty |
| 4 | 682 | 0.76 | 0.82 | 55 | ATP |
| 5 | 166 | 0.75 | 0.92 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3744 Ų buried · 37 hydrogen bonds · protein-protein
- A–M · 1231 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–T · 1175 Ų buried · 11 hydrogen bonds · protein-nucleic
- N–T · 1064 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–N · 845 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6TZ2 · In situ structure of BmCPV RNA-dependent RNA polymerase at 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 6TZ2 · PDBe 6TZ2 · UniProt Q993A4 · UniProt Q9IR43
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