Research workbench
Thermus thermophilus RNA polymerase de novo transcription initiation complex
Analyse Thermus thermophilus RNA polymerase de novo transcription initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q4Z
- Type
- protein + DNA
- Length
- 3,547 residues
- Chains
- 8
- 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
- Q9Z9H6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- ATP, 2TM, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 22% helix, 42% strand | Q9Z9H6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 22% helix, 42% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 29% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1494 | 37% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 49% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor siga | protein | 346 | 70% helix, 1% strand | Q5SKW1 |
| G | DNA (5'- D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*GP*CP*CP*A)- 3') | dna | 18 | — | — |
| H | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains C, D, G
- 2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains C, D, G
- MG · Magnesium ion · metal · 3 copies · chains D, B
- ZN · Zinc ion · metal · 2 copies · 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 | 1014 | 0.87 | 0.88 | 125 | empty |
| 2 | 1081 | 0.86 | 0.87 | 104 | empty |
| 3 | 1128 | 0.85 | 0.85 | 94 | empty |
| 4 | 598 | 0.78 | 0.84 | 87 | ATP, MG, 2TM |
| 5 | 609 | 0.78 | 0.83 | 70 | empty |
Interfaces
18 interfaces between chains.
- C–D · 8987 Ų buried · 134 hydrogen bonds · protein-protein
- D–F · 4078 Ų buried · 59 hydrogen bonds · protein-protein
- C–F · 2468 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2358 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2123 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4Q4Z · Thermus thermophilus RNA polymerase de novo transcription initiation complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q8RQE9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q8RQE9) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q9Z9H6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9Z9H6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9Z9H6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 4Q4Z · PDBe 4Q4Z · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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