Research workbench
Structure of the apo-state of the bacteriophage phikz non-virion RNA polymerase - class including clamp
Analyse Structure of the apo-state of the bacteriophage phikz non-virion RNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OGP
- Type
- protein
- Length
- 2,144 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHIKZ055,PHIKZ056.1; PHIKZ068; PHIKZ071,DNA-directed RNA polymerase; PHIKZ074; PHIKZ123
- EC
- 2.7.7.6
- UniProt
- Q8SDA7, L7T138, Q8SD94, Q8SD91, Q8SD89, Q8SD88, Q8SD39
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 34% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PHIKZ055,PHIKZ056.1 | protein | 361 | 33% helix, 11% strand | Q8SDA7, L7T138 |
| B | PHIKZ068 | protein | 203 | 52% helix, 4% strand | Q8SD94 |
| C | PHIKZ071,DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 693 | 27% helix, 20% strand | Q8SD91, Q8SD89 |
| D | PHIKZ074 | protein | 510 | 39% helix, 5% strand | Q8SD88 |
| E | PHIKZ123 | protein | 377 | 32% helix, 12% 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.84 | 0.85 | 78 | empty |
| 2 | 1039 | 0.79 | 0.80 | 81 | empty |
| 3 | 996 | 0.79 | 0.80 | 107 | empty |
| 4 | 967 | 0.77 | 0.79 | 77 | empty |
| 5 | 92 | 0.73 | 0.95 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–C · 4624 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 4022 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 3903 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 3254 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1913 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7OGP · Structure of the apo-state of the bacteriophage PhiKZ non-virion RNA polymerase - class… · 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 Q8SDA7
- Every structure of UniProt L7T138
- Every structure of UniProt Q8SD94
- Every structure of UniProt Q8SD91
- Every structure of UniProt Q8SD89
- Every structure of UniProt Q8SD88
- Every structure of UniProt Q8SD39
- Elsewhere: RCSB PDB 7OGP · PDBe 7OGP · UniProt Q8SDA7 · UniProt L7T138 · UniProt Q8SD94 · UniProt Q8SD91 · UniProt Q8SD89 · UniProt Q8SD88 · UniProt Q8SD39
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