Research workbench
Crystal structure of the T. thermophilus RNA polymerase elongation complex
Analyse Crystal structure of the T. thermophilus RNA polymerase elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O5I
- Type
- protein + DNA + RNA
- Length
- 6,054 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*G P*CP*GP*CP*CP*G)-3'…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, X | 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*G P*CP*GP*CP*CP*G)-3' | dna | 23 | — | — |
| H, Y | 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' | rna | 16 | — | — |
| I, Z | 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' | dna | 13 | — | — |
| A, B, K, L | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 229 | 20% helix, 38% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 26% helix, 22% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1303 | 39% helix, 14% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase omega chain (EC 2.7.7.6) | protein | 95 | 46% helix, 4% strand | Q8RQE7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, N
- MG · Magnesium ion · metal · 2 copies · chains H, D, Y, 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 | 1000 | 0.86 | 0.87 | 91 | empty |
| 2 | 1098 | 0.86 | 0.87 | 103 | empty |
| 3 | 939 | 0.85 | 0.87 | 89 | empty |
| 4 | 511 | 0.84 | 0.90 | 64 | empty |
| 5 | 1076 | 0.84 | 0.85 | 96 | empty |
Interfaces
34 interfaces between chains.
- C–D · 9310 Ų buried · 131 hydrogen bonds · protein-protein
- M–N · 9212 Ų buried · 120 hydrogen bonds · protein-protein
- A–C · 2447 Ų buried · 49 hydrogen bonds · protein-protein
- N–O · 2447 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 2415 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2O5I · Crystal structure of the T. thermophilus RNA polymerase elongation complex · the same entry in another collection · chain O against O, 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 2O5I · PDBe 2O5I · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.