MolNFT v1 · #98785 · protein
Crystal structure analysis of the E.COLI holoenzyme
4LK1 · DNA-directed RNA polymerase subunit alpha: “Crystal structure analysis of the E.COLI holoenzyme”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #98785 on GenesisL1: 3D structure, binding sites…
- PDB
- 4LK1
- Type
- protein
- Length
- 7,318 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 0.84
Structure
x-ray diffraction · 11 distinct chains · 39% helix, 16% 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, 31% strand | C9QXI7 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 18% helix, 29% 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 | 42% helix, 14% 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 | 542 | 65% helix, 2% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 19% helix, 30% strand | C9QXI7 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 30% strand | C9QXI7 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 37% helix, 16% 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 | 539 | 65% helix, 2% 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 | 906 | 0.84 | 0.85 | 79 | empty |
| 2 | 655 | 0.82 | 0.86 | 85 | empty |
| 3 | 696 | 0.81 | 0.85 | 89 | empty |
| 4 | 1141 | 0.81 | 0.82 | 138 | empty |
| 5 | 890 | 0.80 | 0.82 | 87 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8169 Ų buried · 112 hydrogen bonds · protein-protein
- I–J · 8166 Ų buried · 112 hydrogen bonds · protein-protein
- J–L · 3341 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 3207 Ų buried · 23 hydrogen bonds · protein-protein
- I–L · 2108 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4LK1 · 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 4LK1 · PDBe 4LK1 · UniProt C9QXI7 · UniProt C9QV90 · UniProt C5A0S8 · UniProt C9QUL2 · UniProt P00579
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.