MolNFT v1 · #109057 · protein
Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a GREA/GFH1 chimeric protein)
4WQT · DNA-directed RNA polymerase subunit alpha: “Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a GREA/GFH1 chimeric…”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88).…
- PDB
- 4WQT
- Type
- protein
- Length
- 9,299 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 10 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 20% helix, 26% strand | Q5SHR6 |
| B, L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 21% helix, 33% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1080 | 25% helix, 19% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 36% helix, 12% strand | Q8RQE8 |
| E, J, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 93 | 44% helix, 3% strand | Q8RQE7 |
| H | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1081 | 25% helix, 20% strand | Q8RQE9 |
| I | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1318 | 36% helix, 12% strand | Q8RQE8 |
| K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 20% helix, 28% strand | Q5SHR6 |
| N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1323 | 36% helix, 12% strand | Q8RQE8 |
| X, Y, Z | RNA cleavage stimulating factor (GREA/GFH1 chimeric protein gre-C1) | protein | 154 | 36% helix, 15% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains D, I, N
- MG · Magnesium ion · metal · 3 copies · chains D, I, 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 | 1173 | 0.88 | 0.89 | 129 | empty |
| 2 | 1115 | 0.87 | 0.88 | 107 | empty |
| 3 | 1052 | 0.86 | 0.87 | 100 | empty |
| 4 | 1130 | 0.85 | 0.86 | 142 | MG |
| 5 | 796 | 0.85 | 0.87 | 92 | empty |
Interfaces
41 interfaces between chains.
- M–N · 8236 Ų buried · 101 hydrogen bonds · protein-protein
- H–I · 8121 Ų buried · 86 hydrogen bonds · protein-protein
- C–D · 7818 Ų buried · 94 hydrogen bonds · protein-protein
- D–X · 2389 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 2303 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Elsewhere: RCSB PDB 4WQT · PDBe 4WQT · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7
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