Research workbench
Thermus aquaticus DELTA1.1-sigmaa HOLOENZYME/DOWNSTREAM-fork promoter complex with an open clamp
Analyse Thermus aquaticus DELTA1.1-sigmaa HOLOENZYME/DOWNSTREAM-fork promoter complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TJG
- Type
- protein + DNA
- Length
- 3,474 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4, Q9EZJ8
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 19% helix, 38% strand | Q9KWU8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 27% helix, 27% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1475 | 36% helix, 25% strand | Q9KWU6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 48% helix, 10% strand | Q9EVV4 |
| F | RNA polymerase sigma factor siga | protein | 334 | 71% helix, 1% strand | Q9EZJ8 |
| G | DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3') | dna | 10 | — | — |
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 | 747 | 0.86 | 0.89 | 79 | empty |
| 2 | 1085 | 0.84 | 0.85 | 96 | empty |
| 3 | 506 | 0.75 | 0.83 | 70 | empty |
| 4 | 231 | 0.74 | 0.88 | 36 | empty |
| 5 | 681 | 0.73 | 0.80 | 73 | empty |
Interfaces
11 interfaces between chains.
- C–D · 8515 Ų buried · 117 hydrogen bonds · protein-protein
- D–F · 3908 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 2326 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2080 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1919 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5TJG · Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an… · the same entry in another collection · chain G against G, 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 0.98
- Q9EVV4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q9EVV4) · a predicted model of the same protein · chain E against A, TM-score 0.97
- Q9KWU8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9KWU8) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q9EZJ8 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q9EZJ8) · a predicted model of the same protein · chain F against A, TM-score 0.93
- Q9KWU6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q9KWU6) · a predicted model of the same protein · chain D against A, TM-score 0.91
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
- Every structure of UniProt Q9EZJ8
- Elsewhere: RCSB PDB 5TJG · PDBe 5TJG · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4 · UniProt Q9EZJ8
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