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
- 5NWT
- Type
- protein
- Length
- 3,707 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800, R4YEY9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 307 | 29% helix, 21% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 22% helix, 31% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1318 | 30% helix, 17% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 37% helix, 12% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 78 | 69% helix, 0% strand | P0A800 |
| M | RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 factor | protein | 431 | 43% helix, 4% strand | R4YEY9 |
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 | 945 | 0.88 | 0.90 | 138 | empty |
| 2 | 425 | 0.85 | 0.93 | 63 | empty |
| 3 | 1162 | 0.84 | 0.85 | 137 | empty |
| 4 | 1024 | 0.81 | 0.83 | 118 | empty |
| 5 | 517 | 0.81 | 0.88 | 99 | empty |
Interfaces
11 interfaces between chains.
- C–D · 6337 Ų buried · 53 hydrogen bonds · protein-protein
- D–M · 1599 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1187 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1006 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 882 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 5NWT · Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex · the same entry in another collection · chain M against M, 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 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 0.91
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt R4YEY9
- Elsewhere: RCSB PDB 5NWT · PDBe 5NWT · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt R4YEY9
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