Research workbench
Escherichia COLI RNA polymerase and ureidothiophene-2-carboxylic acid complex
Analyse Escherichia COLI RNA polymerase and ureidothiophene-2-carboxylic acid complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJS
- Type
- protein
- Length
- 7,106 residues
- Chains
- 12
- 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
- P0A7Z4, P0A8V4, P0A8T7, P0A802, Q0P6L9
- Ligands
- QZY, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 234 | 22% helix, 33% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 301 | 26% helix, 26% strand | P0A7Z4 |
| C, H | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1336 | 28% helix, 18% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1164 | 38% helix, 10% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 61% helix, 0% strand | P0A802 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 22% helix, 31% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1160 | 38% helix, 10% strand | P0A8T7 |
| J | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 57% helix, 0% strand | P0A802 |
| X | RNA polymerase sigma factor rpod | protein | 471 | 64% helix, 1% strand | Q0P6L9 |
| Y | RNA polymerase sigma factor rpod | protein | 475 | 65% helix, 1% strand | Q0P6L9 |
Ligands and binding sites
- QZY · 3-{[benzyl(ethyl)carbamoyl]amino}-5-(4-phenoxyphenyl) thiophene-2-carboxylic acid · ligand · chains C, D
- ZN · Zinc ion · metal · 4 copies · chains D, I
- MG · Magnesium ion · metal · 2 copies · chains D, I
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 | 1031 | 0.87 | 0.88 | 118 | empty |
| 2 | 1086 | 0.84 | 0.85 | 76 | QZY |
| 3 | 586 | 0.83 | 0.88 | 58 | empty |
| 4 | 968 | 0.81 | 0.83 | 71 | empty |
| 5 | 858 | 0.81 | 0.83 | 91 | empty |
Interfaces
19 interfaces between chains.
- H–I · 8219 Ų buried · 109 hydrogen bonds · protein-protein
- C–D · 8129 Ų buried · 103 hydrogen bonds · protein-protein
- D–X · 2961 Ų buried · 29 hydrogen bonds · protein-protein
- I–Y · 2897 Ų buried · 28 hydrogen bonds · protein-protein
- C–X · 2179 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6VJS · Escherichia coli RNA polymerase and ureidothiophene-2-carboxylic acid complex · the same entry in another collection · chain Y against Y, 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 P0A7Z4
- Every structure of UniProt P0A8V4
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Elsewhere: RCSB PDB 6VJS · PDBe 6VJS · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9
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