MolNFT v1 · #102336 · protein + DNA
Crystal structure of thermus thermophilus pre-insertion substrate complex for de novo transcription initiation
4OIO · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus pre-insertion substrate complex for de novo transcription initiation”. X-ray diffraction, 4 ligands (ATP, 2TM, ZN), 20 pockets (best druggability…
- PDB
- 4OIO
- Type
- protein + DNA
- Length
- 3,516 residues
- Chains
- 8
- 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
- ATP, 2TM, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 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 | 22% helix, 38% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 23% helix, 43% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 30% helix, 26% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1479 | 36% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 48% helix, 9% strand | Q8RQE7 |
| F | DNA directed RNA polymerase sigma factor a | protein | 344 | 68% helix, 1% 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 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains C, D, G
- 2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains C, D, G
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 2 copies · chains D, C
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 | 1082 | 0.86 | 0.87 | 99 | empty |
| 2 | 469 | 0.85 | 0.93 | 62 | empty |
| 3 | 1155 | 0.84 | 0.85 | 99 | empty |
| 4 | 449 | 0.81 | 0.89 | 55 | empty |
| 5 | 653 | 0.81 | 0.85 | 69 | empty |
Interfaces
18 interfaces between chains.
- C–D · 9134 Ų buried · 129 hydrogen bonds · protein-protein
- D–F · 3989 Ų buried · 40 hydrogen bonds · protein-protein
- C–F · 2549 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 2308 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2043 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4OIO · Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo… · the same entry in another collection · chain F against F, 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 0.97
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 4OIO · PDBe 4OIO · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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