Research workbench
X-ray crystal structur of escherichia COLI RNA polymerase SIGMA70 holoenzyme
Analyse X-ray crystal structur of escherichia COLI RNA polymerase SIGMA70 holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YG2
- Type
- protein
- Length
- 7,085 residues
- Chains
- 12
- 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
- P0A7Z6, P0A8V4, P0A8T8, P0A802, P00579
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 319 | 27% helix, 27% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 17% helix, 33% strand | P0A7Z6 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 23% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1166 | 41% helix, 14% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 61% helix, 0% strand | P0A802 |
| F | RNA polymerase sigma factor rpod | protein | 468 | 62% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 20% helix, 36% strand | P0A7Z6 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 17% helix, 36% strand | P0A7Z6 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1155 | 43% helix, 14% strand | P0A8T8 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 62% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 62% helix, 3% strand | P00579 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, D, I, J
- ZN · Zinc ion · metal · 4 copies · chains D, J
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 | 0.84 | 0.85 | 96 | empty |
| 2 | 577 | 0.81 | 0.87 | 60 | empty |
| 3 | 703 | 0.81 | 0.85 | 81 | empty |
| 4 | 537 | 0.80 | 0.86 | 63 | empty |
| 5 | 770 | 0.78 | 0.81 | 93 | empty |
Interfaces
21 interfaces between chains.
- I–J · 8099 Ų buried · 96 hydrogen bonds · protein-protein
- C–D · 8075 Ų buried · 99 hydrogen bonds · protein-protein
- J–L · 2712 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 2688 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2121 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4YG2 · X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme · the same entry in another collection · chain K against K, 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 P0A7Z6
- Every structure of UniProt P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A802
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4YG2 · PDBe 4YG2 · UniProt P0A7Z6 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A802 · UniProt P00579
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