MolNFT v1 · #102337 · protein + DNA
Crystal structure of thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and cmpcpp
4OIP · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and…”. X-ray diffraction, 4 ligands (MB8, ATP, MG), 20 pockets (best druggability…
- PDB
- 4OIP
- Type
- protein + DNA
- Length
- 3,543 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, ATP, 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 | 231 | 22% helix, 42% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 22% helix, 39% 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 | 1486 | 37% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 50% helix, 12% strand | Q8RQE7 |
| F | DNA directed RNA polymerase sigma factor a | protein | 346 | 68% helix, 2% strand | Q5SKW1 |
| G | 5'-D(*CP*CP*TP*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 C, I
- ATP · Adenosine-5'-triphosphate · ligand · chains C, D
- MG · Magnesium ion · metal · 6 copies · chains B, D, I, C, 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 | 1108 | 0.86 | 0.87 | 106 | empty |
| 2 | 1054 | 0.86 | 0.87 | 107 | empty |
| 3 | 478 | 0.85 | 0.92 | 59 | empty |
| 4 | 583 | 0.81 | 0.87 | 88 | MG |
| 5 | 950 | 0.78 | 0.80 | 89 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8985 Ų buried · 125 hydrogen bonds · protein-protein
- D–F · 4099 Ų buried · 52 hydrogen bonds · protein-protein
- C–F · 2515 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2410 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2050 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 d-amino, 1 covalent (nonstandard, D-amino acid, covalent ligand).
Compared structures
- 4OIP · Crystal structure of Thermus thermophilus transcription initiation complex soaked with… · the same entry in another collection · chain I against I, 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 4OIP · PDBe 4OIP · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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