MolNFT v1 · #104281 · protein + DNA + RNA
Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA
4Q5S · DNA-directed RNA polymerase subunit alpha: “Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA”. X-ray diffraction, 3 ligands (ATP, ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #104281…
- PDB
- 4Q5S
- Type
- protein + DNA + RNA
- Length
- 3,510 residues
- Chains
- 9
- 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, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 19% helix, 36% strand | Q9Z9H6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 22% helix, 41% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 27% helix, 25% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1484 | 35% helix, 23% 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 | 338 | 62% 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 | 14 | — | — |
| H | DNA (5'- D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP* GP*CP*AP*GP*G)-3') | dna | 16 | — | — |
| I | RNA (5'-R(P*CP*UP*CP*AP*C)-3') | rna | 5 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains C, G, I
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D, I
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 | 1071 | 0.86 | 0.87 | 101 | empty |
| 2 | 1043 | 0.85 | 0.86 | 91 | empty |
| 3 | 966 | 0.83 | 0.84 | 77 | empty |
| 4 | 420 | 0.81 | 0.90 | 53 | empty |
| 5 | 451 | 0.79 | 0.87 | 54 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8941 Ų buried · 113 hydrogen bonds · protein-protein
- D–F · 4026 Ų buried · 50 hydrogen bonds · protein-protein
- D–E · 2433 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 2368 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2139 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4Q5S · Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA · the same entry in another collection · chain E against E, 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
- Q8RQE8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q8RQE8) · a predicted model of the same protein · chain D 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 0.97
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 4Q5S · PDBe 4Q5S · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.