MolNFT v1 · #135023 · protein
Re-refinement of thermus thermophilus RNA polymerase
5TMF · DNA-directed RNA polymerase subunit alpha: “Re-refinement of thermus thermophilus RNA polymerase”. X-ray diffraction, 4 ligands (NE6, ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #135023 on GenesisL1: 3D structure…
- PDB
- 5TMF
- Type
- protein
- Length
- 3,538 residues
- Chains
- 6
- 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
- NE6, ZN, MG, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 21% helix, 40% strand | Q9Z9H6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 238 | 16% helix, 39% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1119 | 24% helix, 24% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1504 | 33% helix, 16% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 95 | 43% helix, 6% strand | Q72ID6 |
| F | RNA polymerase sigma factor siga | protein | 351 | 64% helix, 1% strand | Q72L95 |
Ligands and binding sites
- NE6 · Methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2, 4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate · ligand · chains C, D
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, C, 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 | 1048 | 0.86 | 0.87 | 102 | empty |
| 2 | 1125 | 0.86 | 0.87 | 109 | empty |
| 3 | 1059 | 0.85 | 0.85 | 87 | NE6 |
| 4 | 599 | 0.83 | 0.88 | 63 | empty |
| 5 | 510 | 0.80 | 0.87 | 58 | empty |
Interfaces
11 interfaces between chains.
- C–D · 8895 Ų buried · 118 hydrogen bonds · protein-protein
- D–F · 4461 Ų buried · 55 hydrogen bonds · protein-protein
- D–E · 2425 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2029 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1912 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5TMF · Re-refinement of thermus thermophilus RNA polymerase · the same entry in another collection · chain F against F, 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 0.95
- 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 5TMF · PDBe 5TMF · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q72ID6 · UniProt Q72L95
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