MolNFT v1 · #135020 · protein
Re-refinement of thermus thermopiles DNA-directed RNA polymerase structure
5TMC · DNA-directed RNA polymerase subunit alpha: “Re-refinement of thermus thermopiles DNA-directed RNA polymerase structure”. X-ray diffraction, 4 ligands (G4P, MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #135020 on…
- PDB
- 5TMC
- Type
- protein
- Length
- 3,586 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
- Q9Z9H6, Q8RQE9, Q8RQE8, Q72ID6, Q72L95
- Ligands
- G4P, MG, ZN, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 28% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 20% helix, 33% strand | Q9Z9H6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 238 | 18% helix, 29% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1119 | 21% helix, 23% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1504 | 30% helix, 16% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 95 | 40% helix, 6% strand | Q72ID6 |
| F | RNA polymerase sigma factor siga | protein | 351 | 55% helix, 1% strand | Q72L95 |
| Z | Unknown protein | protein | 48 | 23% helix, 0% strand | — |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · chains C, D
- MG · Magnesium ion · metal · 4 copies · chains C, D
- ZN · Zinc ion · metal · 2 copies · chains D
- PO4 · Phosphate ion · ion · chains A
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 | 895 | 0.86 | 0.88 | 96 | empty |
| 2 | 1185 | 0.86 | 0.87 | 121 | empty |
| 3 | 967 | 0.86 | 0.87 | 97 | empty |
| 4 | 670 | 0.83 | 0.87 | 93 | MG |
| 5 | 412 | 0.81 | 0.89 | 53 | empty |
Interfaces
11 interfaces between chains.
- C–D · 8994 Ų buried · 109 hydrogen bonds · protein-protein
- D–F · 4471 Ų buried · 61 hydrogen bonds · protein-protein
- D–E · 2324 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2043 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 1965 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5TMC · Re-refinement of Thermus thermopiles DNA-directed RNA polymerase structure · the same entry in another collection · chain Z against Z, TM-score 1.00
- 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 0.96
- Q72ID6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q72ID6) · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q72L95 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q72L95) · a predicted model of the same protein · chain F against A, TM-score 0.86
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 Q72ID6
- Every structure of UniProt Q72L95
- Elsewhere: RCSB PDB 5TMC · PDBe 5TMC · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q72ID6 · UniProt Q72L95
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