Research workbench
X-ray structure of the phage AR9 non-virion RNA polymerase core
Analyse X-ray structure of the phage AR9 non-virion RNA polymerase core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S00
- Type
- protein
- Length
- 4,145 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase beta subunit; DNA-directed RNA polymerase; DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- A0A172JI16, A0A172JHZ2, A0A172JI62, A0A172JIH0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| c, e | DNA-directed RNA polymerase beta subunit | protein | 484 | 39% helix, 23% strand | A0A172JI16 |
| C, E | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 640 | 35% helix, 24% strand | A0A172JHZ2 |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 481 | 52% helix, 8% strand | A0A172JI62 |
| d, f | DNA-directed RNA polymerase beta' subunit | protein | 410 | 44% helix, 17% strand | A0A172JIH0 |
| F | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 596 | 45% helix, 13% strand | A0A172JI62 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D, F
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 | 1110 | 0.85 | 0.86 | 126 | empty |
| 2 | 1006 | 0.84 | 0.84 | 86 | empty |
| 3 | 1167 | 0.82 | 0.83 | 86 | empty |
| 4 | 474 | 0.77 | 0.85 | 45 | empty |
| 5 | 736 | 0.76 | 0.81 | 72 | empty |
Interfaces
16 interfaces between chains.
- E–f · 4592 Ų buried · 51 hydrogen bonds · protein-protein
- C–d · 4587 Ų buried · 46 hydrogen bonds · protein-protein
- c–C · 3794 Ų buried · 46 hydrogen bonds · protein-protein
- e–E · 3640 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 3085 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 7S00 · X-ray structure of the phage AR9 non-virion RNA polymerase core · the same entry in another collection · chain c against c, 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 A0A172JI16
- Every structure of UniProt A0A172JHZ2
- Every structure of UniProt A0A172JI62
- Every structure of UniProt A0A172JIH0
- Elsewhere: RCSB PDB 7S00 · PDBe 7S00 · UniProt A0A172JI16 · UniProt A0A172JHZ2 · UniProt A0A172JI62 · UniProt A0A172JIH0
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