MolNFT v1 · #157590 · protein + DNA
EM structure of the DNA wrapping in bacterial open transcription initiation complex
6N4C · RNA polymerase sigma factor rpod: “EM structure of the DNA wrapping in bacterial open transcription initiation complex”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #157590 on GenesisL1: 3D structure, binding…
- 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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