MolNFT v1 · #136085 · protein
Structure of sigman-holoenzyme
5UI8 · DNA-directed RNA polymerase subunit alpha: “Structure of sigman-holoenzyme”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #136085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UI8
- Type
- protein
- Length
- 3,536 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
- P0A7Z6, B7MIX3, P0A8T8, B7MFL0, A0A0J4U551
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 309 | 27% helix, 20% strand | P0A7Z6 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 18% helix, 30% strand | P0A7Z6 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1217 | 30% helix, 20% strand | B7MIX3 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1336 | 35% helix, 16% strand | P0A8T8 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 57% helix, 0% strand | B7MFL0 |
| M | RNA polymerase sigma-54 factor | protein | 380 | 51% helix, 4% strand | A0A0J4U551 |
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 | 942 | 0.83 | 0.85 | 80 | empty |
| 2 | 1019 | 0.80 | 0.81 | 79 | empty |
| 3 | 892 | 0.78 | 0.81 | 77 | empty |
| 4 | 440 | 0.76 | 0.85 | 55 | empty |
| 5 | 863 | 0.74 | 0.79 | 82 | empty |
Interfaces
11 interfaces between chains.
- I–J · 7980 Ų buried · 107 hydrogen bonds · protein-protein
- J–M · 2064 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1918 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1734 Ų buried · 23 hydrogen bonds · protein-protein
- I–M · 1599 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5UI8 · structure of sigmaN-holoenzyme · the same entry in another collection · chain M against M, TM-score 1.00
- B7MIX3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B7MIX3) · a predicted model of the same protein · chain I against A, TM-score 0.96
- P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain H against A, TM-score 0.96
- B7MFL0 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (B7MFL0) · a predicted model of the same protein · chain K against A, TM-score 0.93
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain J 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 P0A7Z6
- Every structure of UniProt B7MIX3
- Every structure of UniProt P0A8T8
- Every structure of UniProt B7MFL0
- Every structure of UniProt A0A0J4U551
- Elsewhere: RCSB PDB 5UI8 · PDBe 5UI8 · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt A0A0J4U551
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