MolNFT v1 · #30674 · protein
Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin
2A68 · DNA-directed RNA polymerase alpha chain: “Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin”. X-ray diffraction, 3 ligands (RBT, MG, ZN), 20 pockets (best druggability 0.86).…
- PDB
- 2A68
- 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
- RBT, 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, 39% 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 (EC 2.7.7.6) | protein | 95 | 45% helix, 3% strand | — |
| F, P | RNA polymerase sigma factor rpod | protein | 345 | 68% helix, 1% strand | — |
Ligands and binding sites
- RBT · Rifabutin · ligand · 2 copies · chains C, F, M, P
- MG · Magnesium ion · metal · 562 copies · chains A, B, C, 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 | 913 | 0.86 | 0.88 | 88 | MG |
| 2 | 818 | 0.85 | 0.87 | 74 | MG |
| 3 | 1053 | 0.85 | 0.85 | 84 | MG |
| 4 | 529 | 0.84 | 0.90 | 61 | MG |
| 5 | 724 | 0.83 | 0.86 | 79 | MG |
Interfaces
20 interfaces between chains.
- C–D · 9401 Ų buried · 132 hydrogen bonds · protein-protein
- M–N · 8923 Ų buried · 119 hydrogen bonds · protein-protein
- N–P · 4262 Ų buried · 62 hydrogen bonds · protein-protein
- D–F · 3930 Ų buried · 60 hydrogen bonds · protein-protein
- N–O · 2452 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2A68 · 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 2A68 · PDBe 2A68 · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8
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