Research workbench
Crystal structure of P23-45 GP39 (6-109) bound to thermus thermophilus RNA polymerase beta-flap domain
Analyse Crystal structure of P23-45 GP39 (6-109) bound to thermus thermophilus RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WOE
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit beta; Putative uncharacterized protein
- EC
- 2.7.7.6
- UniProt
- Q8RQE9, A7XX65
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 130 | 11% helix, 39% strand | Q8RQE9 |
| B, D | Putative uncharacterized protein | protein | 104 | 8% helix, 42% strand | A7XX65 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.65 | 0.78 | 42 | empty |
| 2 | 319 | 0.60 | 0.77 | 38 | empty |
| 3 | 50 | 0.53 | 0.89 | 12 | empty |
| 4 | 241 | 0.52 | 0.76 | 28 | empty |
| 5 | 127 | 0.47 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1067 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1013 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 593 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3WOE · Crystal structure of P23-45 gp39 (6-109) bound to Thermus thermophilus RNA polymerase… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.84
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 Q8RQE9
- Every structure of UniProt A7XX65
- Elsewhere: RCSB PDB 3WOE · PDBe 3WOE · UniProt Q8RQE9 · UniProt A7XX65
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