MolNFT v1 · #102339 · protein + DNA
Crystal structure of thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin sv
4OIR · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077…”. X-ray diffraction, 4 ligands (MB8, RFV, MG), 20 pockets (best druggability…
- PDB
- 4OIR
- Type
- protein + DNA
- Length
- 3,542 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
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- MB8, RFV, MG, ZN
- Pockets
- 20 · best druggability 0.87
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 | 231 | 22% helix, 41% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 22% helix, 40% strand | Q5SHR6 |
| 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 | 1485 | 37% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 51% helix, 11% strand | Q8RQE7 |
| F | DNA directed RNA polymerase sigma factor a | protein | 346 | 68% helix, 1% strand | Q5SKW1 |
| G | 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP* GP*GP*G)-3' | dna | 16 | — | — |
| H | 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 | 24 | — | — |
| I | GE23077 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- MB8 · (2Z)-2-methylbut-2-enoic acid · ligand · chains G, I
- RFV · rifamycin SV · ligand · chains C, F
- MG · Magnesium ion · metal · 4 copies · chains B, D, I, F
- 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 | 1107 | 0.87 | 0.88 | 118 | empty |
| 2 | 1098 | 0.86 | 0.87 | 98 | empty |
| 3 | 1104 | 0.85 | 0.86 | 97 | empty |
| 4 | 756 | 0.77 | 0.81 | 64 | empty |
| 5 | 453 | 0.74 | 0.83 | 46 | empty |
Interfaces
21 interfaces between chains.
- C–D · 9067 Ų buried · 128 hydrogen bonds · protein-protein
- D–F · 4044 Ų buried · 58 hydrogen bonds · protein-protein
- C–F · 2396 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2355 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2044 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 d-amino, 1 covalent (nonstandard, D-amino acid, covalent ligand).
Compared structures
- 4OIR · Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex… · 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
- 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
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 4OIR · PDBe 4OIR · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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