Research workbench
Cryoem structure of E.COLI RNA polymerase elongation complex
Analyse Cryoem structure of E.COLI 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
- 6ALH
- Type
- protein + DNA + RNA
- Length
- 3,227 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*GP*GP*CP*TP*AP*AP*TP*GP*AP*CP*GP*GP*CP*GP*AP*AP*TP*AP*CP*CP*C)- 3'); DNA…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 8 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*GP*GP*GP*CP*TP*AP*AP*TP*GP*AP*CP*GP*GP*CP*GP*AP*AP*TP*AP*CP*CP*C)- 3') | dna | 22 | — | — |
| B | DNA (29-mer) | dna | 29 | — | — |
| R | RNA (5'-R(P*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') | rna | 10 | — | — |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 22% helix, 33% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 20% helix, 35% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 29% helix, 21% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 35% helix, 16% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 73 | 59% helix, 0% strand | P0A800 |
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 | 909 | 0.86 | 0.88 | 100 | empty |
| 2 | 1069 | 0.85 | 0.86 | 106 | empty |
| 3 | 1121 | 0.81 | 0.82 | 92 | empty |
| 4 | 639 | 0.80 | 0.86 | 55 | empty |
| 5 | 385 | 0.78 | 0.88 | 72 | empty |
Interfaces
16 interfaces between chains.
- I–J · 8480 Ų buried · 92 hydrogen bonds · protein-protein
- G–I · 2023 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1931 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 1324 Ų buried · 18 hydrogen bonds · protein-protein
- B–J · 1137 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6ALH · CryoEM structure of E.coli RNA polymerase elongation complex · the same entry in another collection · chain K against K, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain I against A, TM-score 0.99
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain J against A, TM-score 0.93
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 6ALH · PDBe 6ALH · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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