Research workbench
Crystal structures of bacterial RNA polymerase paused elongation complexes
Analyse Crystal structures of bacterial RNA polymerase paused elongation complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZY
- Type
- protein + DNA + RNA
- Length
- 3,022 residues
- Chains
- 8
- 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 0.87
Structure
x-ray diffraction · 7 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 20% helix, 38% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1083 | 25% helix, 22% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 36% helix, 13% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 93 | 48% helix, 2% strand | Q8RQE7 |
| N | Non-template DNA | dna | 11 | — | — |
| R | RNA transcript | rna | 9 | — | — |
| T | Template DNA | dna | 22 | — | — |
Ligands and binding sites
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 | 1095 | 0.87 | 0.88 | 104 | empty |
| 2 | 1094 | 0.84 | 0.85 | 116 | empty |
| 3 | 191 | 0.81 | 0.95 | 46 | empty |
| 4 | 1005 | 0.80 | 0.82 | 101 | empty |
| 5 | 923 | 0.78 | 0.81 | 89 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8521 Ų buried · 98 hydrogen bonds · protein-protein
- D–E · 2520 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2169 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1633 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1575 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4GZY · Crystal structures of bacterial RNA Polymerase paused elongation complexes · the same entry in another collection · chain T against T, TM-score 1.00
- Q8RQE9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q8RQE9) · a predicted model of the same protein · chain C against A, TM-score 0.95
- 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 0.91
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 4GZY · PDBe 4GZY · 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.