Research workbench
Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex
Analyse Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LK0
- Type
- protein
- Length
- 7,448 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9103
- Source
- Enterobacteria phage T7; Escherichia coli
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- C9QXI7, C9QV90, C5A0S8, C9QUL2, P00579, P03704
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 3.9103 · 12 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 20% helix, 32% strand | C9QXI7 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 19% helix, 30% strand | C9QXI7 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 23% strand | C9QV90 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1345 | 37% helix, 17% strand | C5A0S8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 65% helix, 0% strand | C9QUL2 |
| F | RNA polymerase sigma factor RpoD | protein | 470 | 64% helix, 2% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 20% helix, 31% strand | C9QXI7 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 31% strand | C9QXI7 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1325 | 37% helix, 17% strand | C5A0S8 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | C9QUL2 |
| L | RNA polymerase sigma factor RpoD | protein | 469 | 65% helix, 2% strand | P00579 |
| M, N | Bacterial RNA polymerase inhibitor | protein | 51 | 29% helix, 39% strand | P03704 |
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 | 1186 | 0.85 | 0.86 | 114 | empty |
| 2 | 1131 | 0.84 | 0.85 | 107 | empty |
| 3 | 1037 | 0.82 | 0.83 | 113 | empty |
| 4 | 916 | 0.79 | 0.81 | 88 | empty |
| 5 | 398 | 0.79 | 0.88 | 41 | empty |
Interfaces
25 interfaces between chains.
- C–D · 8161 Ų buried · 114 hydrogen bonds · protein-protein
- I–J · 8067 Ų buried · 109 hydrogen bonds · protein-protein
- D–F · 2885 Ų buried · 25 hydrogen bonds · protein-protein
- J–L · 2813 Ų buried · 27 hydrogen bonds · protein-protein
- D–J · 2001 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4LK0 · Crystal structure analysis of the E.COLI HOLOENZYME/T7 GP2 complex · the same entry in another collection · chain N against N, 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 C9QXI7
- Every structure of UniProt C9QV90
- Every structure of UniProt C5A0S8
- Every structure of UniProt C9QUL2
- Every structure of UniProt P00579
- Every structure of UniProt P03704
- Elsewhere: RCSB PDB 4LK0 · PDBe 4LK0 · UniProt C9QXI7 · UniProt C9QV90 · UniProt C5A0S8 · UniProt C9QUL2 · UniProt P00579 · UniProt P03704
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