Research workbench
Crystal structure of thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin sv
Analyse Crystal structure of thermus thermophilus RNA polymerase transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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