MolNFT v1 · #72457 · protein + DNA
RNA polymerase alpha C-terminal domain (E. COLI) and sigma region 4 (T. aq. mutant) bound to (up,-35 element) DNA
3N97 · RNA polymerase sigma factor: “RNA polymerase alpha C-terminal domain (E. COLI) and sigma region 4 (T. aq. mutant) bound to (up,-35 element)…”. X-ray diffraction, 4 pockets (best druggability 0.47). MolNFT v1 #72457 on GenesisL1: 3D…
- PDB
- 3N97
- Type
- protein + DNA
- Length
- 295 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase sigma factor; DNA-directed RNA polymerase subunit alpha; DNA (5'…
- EC
- 2.7.7.6
- UniProt
- Q9EZJ8, P0A7Z4
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase sigma factor | protein | 53 | 66% helix, 0% strand | Q9EZJ8 |
| D | RNA polymerase sigma factor | protein | 50 | 68% helix, 0% strand | Q9EZJ8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 75 | 47% helix, 3% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 74 | 47% helix, 3% strand | P0A7Z4 |
| M | DNA (5'- D(*TP*GP*GP*AP*AP*AP*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*CP*AP*TP*GP*G)- 3') | dna | 22 | — | — |
| N | DNA (5'- D(*CP*CP*AP*TP*GP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*TP*TP*CP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains C, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.47 | 0.73 | 31 | empty |
| 2 | 102 | 0.40 | 0.77 | 16 | empty |
| 3 | 112 | 0.38 | 0.74 | 21 | empty |
| 4 | 123 | 0.35 | 0.72 | 15 | empty |
Interfaces
10 interfaces between chains.
- M–N · 918 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- A–D · 550 Ų buried · 2 hydrogen bonds · protein-protein
- A–N · 368 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–M · 354 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–N · 244 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3N97 · RNA polymerase alpha C-terminal domain (E. coli) and sigma region 4 (T. aq. mutant) bound… · the same entry in another collection · chain N against N, TM-score 1.00
- Q9EZJ8 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q9EZJ8) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q9EZJ8
- Every structure of UniProt P0A7Z4
- Elsewhere: RCSB PDB 3N97 · PDBe 3N97 · UniProt Q9EZJ8 · UniProt P0A7Z4
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