Research workbench
Taq RNA polymerase-sorangicin complex
Analyse Taq RNA polymerase-sorangicin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YNJ
- Type
- protein
- Length
- 3,151 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase alpha chain; DNA-directed RNA polymerase beta chain…
- EC
- 2.7.7.6
- UniProt
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4
- Ligands
- SRN, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 230 | 20% helix, 30% strand | Q9KWU8 |
| B | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 225 | 21% helix, 34% strand | Q9KWU8 |
| C | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1114 | 24% helix, 21% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1238 | 30% helix, 20% strand | Q9KWU6 |
| J | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 249 | 37% helix, 15% strand | Q9KWU6 |
| K | DNA-directed RNA polymerase omega chain (EC 2.7.7.6) | protein | 95 | 37% helix, 8% strand | Q9EVV4 |
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 | 599 | 0.85 | 0.90 | 66 | empty |
| 2 | 315 | 0.73 | 0.86 | 38 | empty |
| 3 | 294 | 0.73 | 0.86 | 29 | empty |
| 4 | 822 | 0.73 | 0.78 | 80 | empty |
| 5 | 661 | 0.71 | 0.78 | 67 | empty |
Interfaces
12 interfaces between chains.
- C–D · 8348 Ų buried · 113 hydrogen bonds · protein-protein
- D–J · 4199 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 2121 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1918 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1489 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1YNJ · Taq RNA polymerase-Sorangicin complex · the same entry in another collection · chain K against K, TM-score 1.00
- Q9KWU7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q9KWU7) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q9KWU8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9KWU8) · a predicted model of the same protein · chain B against A, TM-score 0.94
- Q9KWU6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q9KWU6) · a predicted model of the same protein · chain J against A, TM-score 0.94
- Q9EVV4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q9EVV4) · a predicted model of the same protein · chain K against A, TM-score 0.93
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 Q9KWU8
- Every structure of UniProt Q9KWU7
- Every structure of UniProt Q9KWU6
- Every structure of UniProt Q9EVV4
- Elsewhere: RCSB PDB 1YNJ · PDBe 1YNJ · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4
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