Research workbench
Crystal structure of escherichia COLI RNA polymerase - SIGMA54 holoenzyme complex
Analyse Crystal structure of escherichia COLI RNA polymerase - SIGMA54 holoenzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BYH
- Type
- protein
- Length
- 3,712 residues
- Chains
- 6
- 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
- A0A4S5AL01, P0A8V2, P0A8T7, P0A800, A0A0N9UTC1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 305 | 25% helix, 26% strand | A0A4S5AL01 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 21% helix, 33% strand | A0A4S5AL01 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 31% helix, 17% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1372 | 36% helix, 12% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 67% helix, 0% strand | P0A800 |
| M | RNA polymerase sigma-54 factor | protein | 421 | 43% helix, 1% strand | A0A0N9UTC1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
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 | 700 | 0.87 | 0.91 | 141 | empty |
| 2 | 939 | 0.83 | 0.85 | 142 | empty |
| 3 | 305 | 0.82 | 0.93 | 49 | empty |
| 4 | 822 | 0.81 | 0.84 | 102 | empty |
| 5 | 576 | 0.80 | 0.86 | 99 | empty |
Interfaces
11 interfaces between chains.
- C–D · 5295 Ų buried · 36 hydrogen bonds · protein-protein
- D–M · 1937 Ų buried · 6 hydrogen bonds · protein-protein
- C–M · 1241 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain D 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 A0A4S5AL01
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt A0A0N9UTC1
- Elsewhere: RCSB PDB 5BYH · PDBe 5BYH · UniProt A0A4S5AL01 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt A0A0N9UTC1
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