MolNFT v1 · #157647 · protein + DNA
Escherichia COLI RNA polymerase SIGMA70-holoenzyme bound to upstream fork promoter DNA
6N62 · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI RNA polymerase SIGMA70-holoenzyme bound to upstream fork promoter DNA”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #157647 on…
- PDB
- 6N62
- Type
- protein + DNA
- Length
- 3,611 residues
- Chains
- 8
- 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
- P0A7Z6, P0A8V4, P0A8T8, P0A802, Q0P6L9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 19% helix, 32% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 27% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1337 | 30% helix, 20% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1226 | 38% helix, 13% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 57% helix, 0% strand | P0A802 |
| F | RNA polymerase sigma factor rpod | protein | 471 | 57% helix, 2% strand | Q0P6L9 |
| N | Non-template strand DNA | dna | 29 | — | — |
| T | Template strand DNA | dna | 24 | — | — |
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 | 1162 | 0.81 | 0.82 | 112 | empty |
| 2 | 769 | 0.81 | 0.85 | 74 | empty |
| 3 | 854 | 0.80 | 0.82 | 99 | empty |
| 4 | 507 | 0.78 | 0.85 | 64 | empty |
| 5 | 1017 | 0.77 | 0.79 | 95 | empty |
Interfaces
13 interfaces between chains.
- C–D · 8316 Ų buried · 121 hydrogen bonds · protein-protein
- D–F · 2659 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2116 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1831 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1781 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6N62 · Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA · the same entry in another collection · chain T against T, TM-score 1.00
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain D against A, TM-score 0.97
- 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
- P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Elsewhere: RCSB PDB 6N62 · PDBe 6N62 · UniProt P0A7Z6 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A802 · UniProt Q0P6L9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.