Research workbench
Sigmas-transcription initiation complex with 4-nt nascent RNA
Analyse Sigmas-transcription initiation complex with 4-nt nascent RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IPM
- Type
- protein + DNA + RNA
- Length
- 3,586 residues
- Chains
- 9
- 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, P13445
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 23% helix, 38% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 24% helix, 39% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 25% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1362 | 38% helix, 18% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 70% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpos | protein | 277 | 68% helix, 2% strand | P13445 |
| 1 | Synthetic non-template strand DNA (50-mer) | dna | 33 | — | — |
| 2 | Synthetic template strand DNA (50-mer) | dna | 33 | — | — |
| 3 | Nascent RNA 4-mer | rna | 4 | — | — |
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 | 735 | 0.83 | 0.86 | 68 | empty |
| 2 | 639 | 0.82 | 0.87 | 62 | empty |
| 3 | 614 | 0.80 | 0.85 | 60 | empty |
| 4 | 285 | 0.79 | 0.91 | 42 | empty |
| 5 | 1163 | 0.78 | 0.80 | 123 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8833 Ų buried · 107 hydrogen bonds · protein-protein
- D–F · 2728 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 2585 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1944 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1771 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5IPM · SigmaS-transcription initiation complex with 4-nt nascent RNA · the same entry in another collection · chain 3 against 3, 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 0.99
- P13445 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpos (P13445) · a predicted model of the same protein · chain F against A, TM-score 0.97
- 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 0.95
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 P13445
- Elsewhere: RCSB PDB 5IPM · PDBe 5IPM · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P13445
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