Research workbench
Crystal structure of E. COLI RNA polymerase in complex with ppgpp
Analyse Crystal structure of E. COLI RNA polymerase in complex with ppgpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKR
- Type
- protein
- Length
- 7,410 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
- K0BPQ3, C9QV90, C5A0S8, C9QUL2, P00579
- Ligands
- G4P, SR, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 22% helix, 39% strand | K0BPQ3 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 23% strand | C9QV90 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1342 | 34% helix, 17% strand | C5A0S8 |
| E, K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 69% helix, 0% strand | C9QUL2 |
| F, L | RNA polymerase sigma factor rpod | protein | 481 | 62% helix, 1% strand | P00579 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1338 | 33% helix, 16% strand | C5A0S8 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains D, E, J, K
- SR · Strontium ion · metal · 8 copies · chains A, C, D, F, I, J
- ZN · Zinc ion · metal · 4 copies · chains D, J
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 | 1006 | 0.87 | 0.88 | 117 | empty |
| 2 | 1157 | 0.85 | 0.86 | 124 | empty |
| 3 | 413 | 0.81 | 0.90 | 46 | empty |
| 4 | 1084 | 0.81 | 0.82 | 87 | empty |
| 5 | 1126 | 0.80 | 0.81 | 91 | empty |
Interfaces
22 interfaces between chains.
- I–J · 9062 Ų buried · 99 hydrogen bonds · protein-protein
- C–D · 8934 Ų buried · 109 hydrogen bonds · protein-protein
- D–F · 2955 Ų buried · 25 hydrogen bonds · protein-protein
- J–L · 2893 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2280 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4JKR · Crystal Structure of E. coli RNA Polymerase in complex with ppGpp · the same entry in another collection · chain L against L, 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 K0BPQ3
- Every structure of UniProt C9QV90
- Every structure of UniProt C5A0S8
- Every structure of UniProt C9QUL2
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4JKR · PDBe 4JKR · UniProt K0BPQ3 · UniProt C9QV90 · UniProt C5A0S8 · UniProt C9QUL2 · UniProt P00579
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