Research workbench
Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin
Analyse Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A69
- Type
- protein
- Length
- 6,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase alpha chain; DNA-directed RNA polymerase beta chain…
- EC
- 2.7.7.6
- UniProt
- Q9Z9H6, Q8RQE9, Q8RQE8
- Ligands
- RPT, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 229 | 21% helix, 40% strand | Q9Z9H6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 25% helix, 20% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1392 | 38% helix, 13% strand | Q8RQE8 |
| E, O | RNA polymerase omega chain | protein | 95 | 47% helix, 3% strand | — |
| F, P | RNA polymerase sigma factor rpod | protein | 345 | 68% helix, 1% strand | — |
Ligands and binding sites
- RPT · Rifapentine · ligand · 2 copies · chains C, F, M
- MG · Magnesium ion · metal · 487 copies · chains A, C, B, D, F, E, K, L, M, N, P, O
- ZN · Zinc ion · metal · 4 copies · chains D, N
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 | 877 | 0.86 | 0.88 | 90 | empty |
| 2 | 489 | 0.85 | 0.91 | 60 | empty |
| 3 | 1118 | 0.85 | 0.85 | 83 | MG |
| 4 | 1187 | 0.84 | 0.85 | 102 | MG |
| 5 | 478 | 0.83 | 0.90 | 74 | empty |
Interfaces
20 interfaces between chains.
- C–D · 9316 Ų buried · 131 hydrogen bonds · protein-protein
- M–N · 8999 Ų buried · 122 hydrogen bonds · protein-protein
- N–P · 4238 Ų buried · 57 hydrogen bonds · protein-protein
- D–F · 3927 Ų buried · 58 hydrogen bonds · protein-protein
- N–O · 2389 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2A69 · Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with… · the same entry in another collection · chain P against P, TM-score 1.00
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 Q9Z9H6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Elsewhere: RCSB PDB 2A69 · PDBe 2A69 · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8
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