Research workbench
Structure of bacteriophage AR9 non-virion rnap polymerase holoenzyme determined by cryo-EM
Analyse Structure of bacteriophage AR9 non-virion rnap polymerase holoenzyme determined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UM1
- Type
- protein
- Length
- 2,247 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase beta' subunit…
- EC
- 2.7.7.6
- UniProt
- A0A172JIC8, A0A172JIH0, A0A172JI16, A0A172JI62, A0A172JHZ2
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit | protein | 173 | 63% helix, 4% strand | A0A172JIC8 |
| d | DNA-directed RNA polymerase beta' subunit | protein | 426 | 41% helix, 15% strand | A0A172JIH0 |
| c | DNA-directed RNA polymerase beta subunit | protein | 484 | 39% helix, 21% strand | A0A172JI16 |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 515 | 53% helix, 5% strand | A0A172JI62 |
| C | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 649 | 33% helix, 21% strand | A0A172JHZ2 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
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 | 922 | 0.83 | 0.84 | 98 | empty |
| 2 | 375 | 0.82 | 0.90 | 42 | empty |
| 3 | 97 | 0.76 | 0.96 | 27 | empty |
| 4 | 203 | 0.76 | 0.90 | 36 | empty |
| 5 | 572 | 0.75 | 0.82 | 41 | empty |
Interfaces
7 interfaces between chains.
- d–C · 4981 Ų buried · 52 hydrogen bonds · protein-protein
- c–C · 3355 Ų buried · 25 hydrogen bonds · protein-protein
- d–D · 3260 Ų buried · 26 hydrogen bonds · protein-protein
- D–C · 3124 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1410 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7UM1 · Structure of bacteriophage AR9 non-virion RNAP polymerase holoenzyme determined by cryo-EM · 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 A0A172JIC8
- Every structure of UniProt A0A172JIH0
- Every structure of UniProt A0A172JI16
- Every structure of UniProt A0A172JI62
- Every structure of UniProt A0A172JHZ2
- Elsewhere: RCSB PDB 7UM1 · PDBe 7UM1 · UniProt A0A172JIC8 · UniProt A0A172JIH0 · UniProt A0A172JI16 · UniProt A0A172JI62 · UniProt A0A172JHZ2
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