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Structural basis for transcription regulation by alarmone ppgpp
Analyse Structural basis for transcription regulation by alarmone ppgpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SMY
- Type
- protein
- Length
- 6,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase alpha chain; DNA-directed RNA polymerase beta chain…
- EC
- 2.7.7.6
- UniProt
- Q9Z9H6, Q8RQE9, Q8RQE8
- Ligands
- G4P, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 229 | 21% helix, 34% strand | Q9Z9H6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 25% helix, 19% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1392 | 38% helix, 12% strand | Q8RQE8 |
| E, O | RNA polymerase omega subunit | protein | 95 | 47% helix, 4% strand | — |
| F, P | Principal sigma factor | protein | 345 | 67% helix, 1% strand | — |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains C, D, M, N
- MG · Magnesium ion · metal · 362 copies · chains A, C, B, D, F, E, M, N
- ZN · Zinc ion · metal · 4 copies · chains D, N
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 | 884 | 0.87 | 0.89 | 85 | MG |
| 2 | 843 | 0.87 | 0.89 | 81 | empty |
| 3 | 972 | 0.87 | 0.88 | 103 | empty |
| 4 | 889 | 0.86 | 0.88 | 93 | MG |
| 5 | 967 | 0.86 | 0.87 | 87 | empty |
Interfaces
20 interfaces between chains.
- C–D · 9161 Ų buried · 122 hydrogen bonds · protein-protein
- M–N · 8716 Ų buried · 120 hydrogen bonds · protein-protein
- N–P · 4423 Ų buried · 58 hydrogen bonds · protein-protein
- D–F · 4286 Ų buried · 48 hydrogen bonds · protein-protein
- N–O · 2452 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1SMY · Structural basis for transcription regulation by alarmone ppGpp · the same entry in another collection · chain P against P, 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 Q9Z9H6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Elsewhere: RCSB PDB 1SMY · PDBe 1SMY · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8
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