Research workbench
Crystal structure of the RNA polymerase holoenzyme from thermus thermophilus at 2.6A resolution
Analyse Crystal structure of the RNA polymerase holoenzyme from thermus thermophilus at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IW7
- Type
- protein
- Length
- 6,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase alpha subunit; RNA polymerase beta subunit; RNA polymerase omega subunit…
- EC
- 2.7.7.6
- UniProt
- Q9Z9H6
- Ligands
- MG, PB
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | RNA polymerase alpha subunit (EC 2.7.7.6) | protein | 229 | 21% helix, 38% strand | Q9Z9H6 |
| C, M | RNA polymerase beta subunit (EC 2.7.7.6) | protein | 1119 | 25% helix, 19% strand | — |
| D, N | RNA polymerase beta subunit (EC 2.7.7.6) | protein | 1392 | 37% helix, 12% strand | — |
| E, O | RNA polymerase omega subunit (EC 2.7.7.6) | protein | 95 | 43% helix, 5% strand | — |
| F, P | RNA polymerase sigma-70 subunit (EC 2.7.7.6) | protein | 345 | 68% helix, 2% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 485 copies · chains A, B, D, C, F, E, K, M, L, N, P, O
- PB · Lead (II) 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 | 961 | 0.88 | 0.90 | 94 | MG |
| 2 | 828 | 0.86 | 0.89 | 98 | MG |
| 3 | 1011 | 0.86 | 0.87 | 100 | MG |
| 4 | 1138 | 0.86 | 0.87 | 99 | MG |
| 5 | 1094 | 0.86 | 0.87 | 104 | MG |
Interfaces
20 interfaces between chains.
- C–D · 9345 Ų buried · 109 hydrogen bonds · protein-protein
- M–N · 8917 Ų buried · 108 hydrogen bonds · protein-protein
- D–F · 4386 Ų buried · 65 hydrogen bonds · protein-protein
- N–P · 4371 Ų buried · 63 hydrogen bonds · protein-protein
- N–O · 2471 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1IW7 · Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A… · 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
- Elsewhere: RCSB PDB 1IW7 · PDBe 1IW7 · UniProt Q9Z9H6
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