MolNFT v1 · #167646 · protein
Virion-packaged DNA-dependent RNA polymerase of crass-like phage PHI14:2
6VR4: “Virion-packaged DNA-dependent RNA polymerase of crass-like phage PHI14:2”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.87). MolNFT v1 #167646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VR4
- Type
- protein
- Length
- 4,332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent RNA polymerase
- UniProt
- S0A2C3
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-dependent RNA polymerase | protein | 2166 | 48% helix, 14% strand | S0A2C3 |
Ligands and binding sites
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 | 930 | 0.87 | 0.89 | 112 | CL |
| 2 | 894 | 0.87 | 0.89 | 111 | CL |
| 3 | 1095 | 0.85 | 0.86 | 116 | CL |
| 4 | 1017 | 0.84 | 0.85 | 91 | empty |
| 5 | 735 | 0.80 | 0.84 | 75 | empty |
Interfaces
1 interface between chains.
- A–B · 967 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 74 modified (engineered).
Compared structures
- 6VR4 · Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2 · 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 S0A2C3
- Elsewhere: RCSB PDB 6VR4 · PDBe 6VR4 · UniProt S0A2C3
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