MolNFT v1 · #159977 · protein + DNA + RNA
X-ray crystal structure of a bacterial reiterative transcription complex of pyrbi promoter
6P71 · DNA-directed RNA polymerase subunit alpha: “X-ray crystal structure of a bacterial reiterative transcription complex of pyrbi promoter”. X-ray diffraction, 3 ligands (UTP, MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6P71
- Type
- protein + DNA + RNA
- Length
- 3,534 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, A0A1J1EUF1, Q72L95
- Ligands
- UTP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 21% helix, 38% strand | Q9Z9H6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 20% helix, 42% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 30% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1500 | 37% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 49% helix, 11% strand | A0A1J1EUF1 |
| F | RNA polymerase sigma factor siga | protein | 346 | 68% helix, 1% strand | Q72L95 |
| G | DNA (5'-D(P*CP*TP*CP*CP*CP*GP*GP*CP*AP*AP*AP*TP*TP*GP*T)- 3') | dna | 15 | — | — |
| H | DNA (5'-D(*TP*AP*TP*AP*AP*TP*CP*GP*AP*GP*CP*CP*GP*GP*GP*A)- 3') | dna | 16 | — | — |
| I | RNA (5'-R(P*AP*AP*UP*U)-3') | rna | 4 | — | — |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · chains C, D, G, I
- MG · Magnesium ion · metal · 2 copies · chains D, I, C
- 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 | 969 | 0.86 | 0.87 | 80 | empty |
| 2 | 1175 | 0.83 | 0.84 | 95 | empty |
| 3 | 322 | 0.82 | 0.92 | 38 | empty |
| 4 | 442 | 0.82 | 0.90 | 71 | MG, UTP |
| 5 | 378 | 0.81 | 0.91 | 42 | empty |
Interfaces
22 interfaces between chains.
- C–D · 9020 Ų buried · 131 hydrogen bonds · protein-protein
- D–F · 4093 Ų buried · 48 hydrogen bonds · protein-protein
- D–E · 2412 Ų buried · 39 hydrogen bonds · protein-protein
- C–F · 2342 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2056 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P71 · X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI promoter · the same entry in another collection · chain I against I, 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 0.97
- 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 0.93
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 A0A1J1EUF1
- Every structure of UniProt Q72L95
- Elsewhere: RCSB PDB 6P71 · PDBe 6P71 · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt A0A1J1EUF1 · UniProt Q72L95
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