MolNFT v1 · #184185 · protein
Structure of the apo-state of the bacteriophage phikz non-virion RNA polymerase
7OGR · Unk helices: “Structure of the apo-state of the bacteriophage phikz non-virion RNA polymerase”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT v1 #184185 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7OGR
- Type
- protein
- Length
- 1,775 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unk helices; PHIKZ055,NON-virion DNA-dependent RNA polymerase subunit beta; PHIKZ068…
- EC
- 2.7.7.6
- UniProt
- Q8SDA7, A0A6H2A8Q1, Q8SD94, Q8SD91, I7DB36, Q8SD88, Q8SD39
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 34% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Unk helices | protein | 32 | 41% helix, 0% strand | — |
| A | PHIKZ055,NON-virion DNA-dependent RNA polymerase subunit beta | protein | 190 | 32% helix, 18% strand | Q8SDA7, A0A6H2A8Q1 |
| B | PHIKZ068 | protein | 197 | 51% helix, 6% strand | Q8SD94 |
| C | PHIKZ071,DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 612 | 27% helix, 23% strand | Q8SD91, I7DB36 |
| D | PHIKZ074 | protein | 373 | 41% helix, 6% strand | Q8SD88 |
| E | PHIKZ123 | protein | 371 | 30% helix, 11% strand | Q8SD39 |
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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.84 | 0.85 | 97 | empty |
| 2 | 946 | 0.76 | 0.79 | 70 | empty |
| 3 | 101 | 0.68 | 0.91 | 18 | empty |
| 4 | 429 | 0.67 | 0.80 | 47 | empty |
| 5 | 566 | 0.64 | 0.76 | 69 | empty |
Interfaces
9 interfaces between chains.
- C–E · 4007 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2986 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2296 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2184 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1640 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7OGR · Structure of the apo-state of the bacteriophage PhiKZ non-virion RNA polymerase · the same entry in another collection · chain X against X, 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 Q8SDA7
- Every structure of UniProt A0A6H2A8Q1
- Every structure of UniProt Q8SD94
- Every structure of UniProt Q8SD91
- Every structure of UniProt I7DB36
- Every structure of UniProt Q8SD88
- Every structure of UniProt Q8SD39
- Elsewhere: RCSB PDB 7OGR · PDBe 7OGR · UniProt Q8SDA7 · UniProt A0A6H2A8Q1 · UniProt Q8SD94 · UniProt Q8SD91 · UniProt I7DB36 · UniProt Q8SD88 · UniProt Q8SD39
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