Research workbench
Crystal structure of the thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the thermus aquaticus RNA polymerase BETA1 domain
Analyse Crystal structure of the thermus thermophilus transcription-repair coupling… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLQ
- Type
- protein
- Length
- 883 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit beta; Transcription-repair coupling factor
- EC
- 2.7.7.6
- UniProt
- Q9KWU7, Q72KB4
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 186 | 40% helix, 25% strand | Q9KWU7 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 180 | 43% helix, 27% strand | Q9KWU7 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 182 | 39% helix, 26% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 185 | 42% helix, 25% strand | Q9KWU7 |
| E | Transcription-repair coupling factor | protein | 38 | 0% helix, 71% strand | Q72KB4 |
| F | Transcription-repair coupling factor | protein | 30 | 0% helix, 60% strand | Q72KB4 |
| G | Transcription-repair coupling factor | protein | 40 | 0% helix, 50% strand | Q72KB4 |
| H | Transcription-repair coupling factor | protein | 42 | 0% helix, 50% strand | Q72KB4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.73 | 0.79 | 83 | empty |
| 2 | 753 | 0.69 | 0.76 | 78 | empty |
| 3 | 239 | 0.52 | 0.76 | 30 | empty |
| 4 | 147 | 0.50 | 0.78 | 21 | empty |
| 5 | 116 | 0.45 | 0.78 | 23 | empty |
Interfaces
13 interfaces between chains.
- A–B · 782 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 773 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 514 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 481 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 476 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3MLQ · Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9KWU7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q9KWU7) · a predicted model of the same protein · chain B 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 Q9KWU7
- Every structure of UniProt Q72KB4
- Elsewhere: RCSB PDB 3MLQ · PDBe 3MLQ · UniProt Q9KWU7 · UniProt Q72KB4
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