Research workbench
SIGM28-transcription initiation complex with specific promoter at the state 2
Analyse SIGM28-transcription initiation complex with specific promoter at the state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PMJ
- Type
- protein + DNA + RNA
- Length
- 3,564 residues
- Chains
- 9
- Method
- electron microscopy
- 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, P0AEM6
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 34% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 19% helix, 30% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 22% strand | B7MIX3 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1337 | 35% helix, 14% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 66% helix, 0% strand | B7MFL0 |
| F | RNA polymerase sigma factor flia | protein | 239 | 62% helix, 0% strand | P0AEM6 |
| 1 | Synthetic nontemplate strand DNA (54-mer) | dna | 54 | — | — |
| 2 | Synthetic template strand DNA (54-mer) | dna | 54 | — | — |
| 3 | Nascent RNA | rna | 3 | — | — |
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 | 1046 | 0.87 | 0.88 | 152 | empty |
| 2 | 562 | 0.86 | 0.92 | 84 | empty |
| 3 | 786 | 0.86 | 0.89 | 112 | empty |
| 4 | 681 | 0.84 | 0.88 | 78 | empty |
| 5 | 386 | 0.83 | 0.92 | 60 | empty |
Interfaces
20 interfaces between chains.
- C–D · 7045 Ų buried · 72 hydrogen bonds · protein-protein
- 1–2 · 1742 Ų buried · 178 hydrogen bonds · nucleic-nucleic
- A–B · 1736 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1564 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1500 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6PMJ · Sigm28-transcription initiation complex with specific promoter at the state 2 · the same entry in another collection · chain 3 against 3, 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 C against A, TM-score 0.95
- P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain B against A, TM-score 0.95
- B7MFL0 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (B7MFL0) · a predicted model of the same protein · chain E 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 P0AEM6
- Elsewhere: RCSB PDB 6PMJ · PDBe 6PMJ · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P0AEM6
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