MolNFT v1 · #159803 · protein
Cryo-EM structure of escherichia COLI SIGMA70 bound rnap polymerase holoenzyme
6P1K · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of escherichia COLI SIGMA70 bound rnap polymerase holoenzyme”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #159803 on…
- PDB
- 6P1K
- Type
- protein
- Length
- 3,693 residues
- Chains
- 6
- Method
- electron microscopy
- 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, P0A8V4, P0A8T7, P0A802, Q0P6L9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 18% helix, 23% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 17% helix, 28% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 26% helix, 16% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1325 | 32% helix, 12% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 57% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 504 | 63% helix, 1% strand | Q0P6L9 |
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 | 739 | 0.81 | 0.85 | 71 | empty |
| 2 | 1167 | 0.78 | 0.80 | 95 | empty |
| 3 | 651 | 0.77 | 0.83 | 56 | empty |
| 4 | 1033 | 0.77 | 0.79 | 82 | empty |
| 5 | 983 | 0.76 | 0.78 | 116 | empty |
Interfaces
9 interfaces between chains.
- I–J · 8065 Ų buried · 39 hydrogen bonds · protein-protein
- J–L · 2764 Ų buried · 20 hydrogen bonds · protein-protein
- I–L · 2312 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1942 Ų buried · 5 hydrogen bonds · protein-protein
- G–I · 1876 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6P1K · Cryo-EM structure of Escherichia coli sigma70 bound RNAP polymerase holoenzyme · the same entry in another collection · chain I against I, TM-score 1.00
- P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain K against A, TM-score 0.89
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 P0A8V4
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Elsewhere: RCSB PDB 6P1K · PDBe 6P1K · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9
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