MolNFT v1 · #10592 · protein
Crystal structure of the RNA polymerase holoenzyme from thermus thermophilus at 2.6A resolution
1IW7 · RNA polymerase alpha subunit: “Crystal structure of the RNA polymerase holoenzyme from thermus thermophilus at 2.6A resolution”. X-ray diffraction, 2 ligands (MG, PB), 20 pockets (best druggability 0.88). MolNFT v1 #10592 on…
- 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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