MolNFT v1 · #109056 · protein + DNA + RNA
Thermus thermophilus RNA polymerase backtracked complex
4WQS · DNA-directed RNA polymerase subunit alpha: “Thermus thermophilus RNA polymerase backtracked complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #109056 on GenesisL1: 3D structure, binding sites…
- PDB
- 4WQS
- Type
- protein + DNA + RNA
- Length
- 5,902 residues
- Chains
- 16
- 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
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 20% helix, 35% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1119 | 26% helix, 22% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1151 | 45% helix, 11% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 95 | 46% helix, 3% strand | Q8RQE7 |
| N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1288 | 39% helix, 14% strand | Q8RQE8 |
| G, X | DNA (28-mer) | dna | 27 | — | — |
| H | RNA (5'- R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3') | rna | 16 | — | — |
| I, Z | DNA (5'- D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)- 3') | dna | 17 | — | — |
| Y | RNA (5'- R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3') | rna | 15 | — | — |
Ligands and binding sites
- 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 | 764 | 0.87 | 0.90 | 95 | empty |
| 2 | 681 | 0.86 | 0.90 | 108 | empty |
| 3 | 722 | 0.86 | 0.90 | 100 | empty |
| 4 | 681 | 0.86 | 0.90 | 79 | empty |
| 5 | 571 | 0.85 | 0.90 | 60 | empty |
Interfaces
36 interfaces between chains.
- C–D · 8974 Ų buried · 132 hydrogen bonds · protein-protein
- M–N · 8110 Ų buried · 110 hydrogen bonds · protein-protein
- N–O · 2447 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2374 Ų buried · 32 hydrogen bonds · protein-protein
- K–M · 2223 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4WQS · Thermus thermophilus RNA polymerase backtracked complex · the same entry in another collection · chain Z against Z, 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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Elsewhere: RCSB PDB 4WQS · PDBe 4WQS · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7
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