Research workbench
Crystal structure analysis of the E.COLI holoenzyme
Analyse Crystal structure analysis of the E.COLI holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LJZ
- Type
- protein
- Length
- 7,167 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
- C9QXI7, C9QV90, C5A0S8, C9QUL2, P00579
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 18% helix, 29% strand | C9QXI7 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 19% helix, 28% 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 | 1166 | 41% helix, 13% strand | C5A0S8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 64% helix, 0% strand | C9QUL2 |
| F | RNA polymerase sigma factor rpod | protein | 470 | 66% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 18% helix, 28% strand | C9QXI7 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 19% helix, 31% strand | C9QXI7 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1325 | 36% helix, 17% strand | C5A0S8 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | C9QUL2 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 66% helix, 3% strand | P00579 |
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 | 591 | 0.82 | 0.88 | 66 | empty |
| 2 | 531 | 0.80 | 0.87 | 60 | empty |
| 3 | 1123 | 0.78 | 0.80 | 90 | empty |
| 4 | 549 | 0.78 | 0.84 | 54 | empty |
| 5 | 914 | 0.77 | 0.80 | 68 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8098 Ų buried · 100 hydrogen bonds · protein-protein
- I–J · 8031 Ų buried · 96 hydrogen bonds · protein-protein
- D–F · 2762 Ų buried · 28 hydrogen bonds · protein-protein
- J–L · 2701 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2026 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4LJZ · Crystal Structure Analysis of the E.coli holoenzyme · 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 C9QXI7
- Every structure of UniProt C9QV90
- Every structure of UniProt C5A0S8
- Every structure of UniProt C9QUL2
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4LJZ · PDBe 4LJZ · UniProt C9QXI7 · UniProt C9QV90 · UniProt C5A0S8 · UniProt C9QUL2 · UniProt P00579
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