Research workbench
Crystal structure of escherichia COLI RNA polymerase in complex with CBRH16-br
Analyse Crystal structure of escherichia COLI RNA polymerase in complex with CBRH16-br in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZH3
- Type
- protein
- Length
- 7,357 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
- 4OD, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 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 | 302 | 28% helix, 26% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 18% helix, 30% strand | P0A7Z4 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1151 | 42% helix, 14% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 64% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 542 | 64% helix, 2% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 20% helix, 34% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 18% helix, 28% strand | P0A7Z4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1319 | 37% helix, 17% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor rpod | protein | 539 | 65% helix, 2% strand | P00579 |
Ligands and binding sites
- 4OD · N'-(3-bromophenyl)-4-fluoro-N-hydroxy-3-(trifluoromethyl)benzenecarboximidamide · ligand · 2 copies · chains C, D, I, J
- ZN · Zinc ion · metal · 4 copies · chains D, J
- MG · Magnesium ion · metal · 2 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 | 1160 | 0.84 | 0.85 | 119 | empty |
| 2 | 1028 | 0.84 | 0.85 | 110 | empty |
| 3 | 1065 | 0.82 | 0.83 | 101 | empty |
| 4 | 1121 | 0.81 | 0.82 | 132 | empty |
| 5 | 1062 | 0.81 | 0.82 | 118 | empty |
Interfaces
21 interfaces between chains.
- C–D · 7976 Ų buried · 109 hydrogen bonds · protein-protein
- I–J · 7970 Ų buried · 110 hydrogen bonds · protein-protein
- J–L · 3246 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 3131 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2113 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4ZH3 · Crystal structure of Escherichia coli RNA polymerase in complex with CBRH16-Br · 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 4ZH3 · PDBe 4ZH3 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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