Research workbench
Crystal structure of escherichia COLI RNA polymerase holoenzyme
Analyse Crystal structure of escherichia COLI RNA polymerase holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MEY
- Type
- protein
- Length
- 7,075 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, P0A8V2, P0A8T7, P0A800, P00579
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 10 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 298 | 26% helix, 29% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 287 | 27% helix, 29% strand | P0A7Z4 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 32% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1147 | 44% helix, 12% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 64% helix, 0% strand | P0A800 |
| F, L | RNA polymerase sigma factor rpod | protein | 464 | 69% helix, 2% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 21% helix, 36% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 20% helix, 36% strand | P0A7Z4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1140 | 44% helix, 12% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 65% helix, 0% strand | P0A800 |
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 | 1040 | 0.85 | 0.86 | 107 | empty |
| 2 | 1098 | 0.85 | 0.85 | 120 | empty |
| 3 | 457 | 0.80 | 0.88 | 82 | empty |
| 4 | 457 | 0.80 | 0.88 | 78 | empty |
| 5 | 571 | 0.79 | 0.85 | 73 | empty |
Interfaces
20 interfaces between chains.
- I–J · 7334 Ų buried · 85 hydrogen bonds · protein-protein
- C–D · 7273 Ų buried · 82 hydrogen bonds · protein-protein
- D–F · 2092 Ų buried · 24 hydrogen bonds · protein-protein
- J–L · 2042 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1988 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4MEY · Crystal structure of Escherichia coli RNA polymerase 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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4MEY · PDBe 4MEY · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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