Research workbench
EM structure of the DNA wrapping in bacterial open transcription initiation complex
Analyse EM structure of the DNA wrapping in bacterial open transcription initiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N4C
- Type
- protein + DNA
- Length
- 4,161 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase sigma factor rpod; DNA-directed RNA polymerase subunit beta; DNA-directed…
- EC
- 2.7.7.6
- UniProt
- P00579, A0A0A0GWV9, A0A369F490, P0A7Z4, P0A800
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 33% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | RNA polymerase sigma factor rpod | protein | 558 | 60% helix, 0% strand | P00579 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 28% helix, 21% strand | A0A0A0GWV9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 33% helix, 16% strand | A0A369F490 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 316 | 22% helix, 19% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 310 | 14% helix, 18% strand | P0A7Z4 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 56% helix, 0% strand | P0A800 |
| a | DNA (94-mer) | dna | 94 | — | — |
| b | DNA (94-mer) | dna | 94 | — | — |
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 | 0.84 | 0.87 | 87 | empty |
| 2 | 1137 | 0.83 | 0.84 | 117 | empty |
| 3 | 565 | 0.80 | 0.87 | 61 | empty |
| 4 | 1074 | 0.80 | 0.82 | 97 | empty |
| 5 | 798 | 0.80 | 0.83 | 79 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8574 Ų buried · 172 hydrogen bonds · protein-protein
- a–b · 4004 Ų buried · 277 hydrogen bonds · nucleic-nucleic
- F–D · 3250 Ų buried · 81 hydrogen bonds · protein-protein
- A–B · 3091 Ų buried · 70 hydrogen bonds · protein-protein
- F–a · 2177 Ų buried · 53 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6N4C · EM structure of the DNA wrapping in bacterial open transcription initiation complex · the same entry in another collection · chain F against F, 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 P00579
- Every structure of UniProt A0A0A0GWV9
- Every structure of UniProt A0A369F490
- Every structure of UniProt P0A7Z4
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 6N4C · PDBe 6N4C · UniProt P00579 · UniProt A0A0A0GWV9 · UniProt A0A369F490 · UniProt P0A7Z4 · UniProt P0A800
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