Research workbench
Structure of thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin
Analyse Structure of thermus thermophilus RNA polymerase holoenzyme in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZYR
- Type
- protein
- Length
- 6,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase alpha chain; DNA-directed RNA polymerase beta chain…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- STD, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 229 | 18% helix, 28% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 22% helix, 20% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase subunit beta' chain (EC 2.7.7.6) | protein | 1392 | 35% helix, 12% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase omega chain | protein | 95 | 43% helix, 3% strand | Q8RQE7 |
| F, P | DNA-directed RNA polymerase sigma chain | protein | 345 | 62% helix, 1% strand | Q5SKW1 |
Ligands and binding sites
- STD · Streptolydigin · ligand · 2 copies · chains C, D, M, N
- ZN · Zinc ion · metal · 4 copies · chains D, N
- MG · Magnesium ion · metal · 2 copies · chains D, N
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 | 1122 | 0.87 | 0.89 | 107 | empty |
| 2 | 533 | 0.87 | 0.93 | 63 | empty |
| 3 | 987 | 0.87 | 0.88 | 79 | empty |
| 4 | 1034 | 0.87 | 0.88 | 110 | empty |
| 5 | 894 | 0.86 | 0.87 | 76 | empty |
Interfaces
20 interfaces between chains.
- C–D · 9090 Ų buried · 118 hydrogen bonds · protein-protein
- M–N · 8698 Ų buried · 109 hydrogen bonds · protein-protein
- N–P · 4348 Ų buried · 58 hydrogen bonds · protein-protein
- D–F · 4336 Ų buried · 63 hydrogen bonds · protein-protein
- N–O · 2479 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ZYR · Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the… · the same entry in another collection · chain D against D, 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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 1ZYR · PDBe 1ZYR · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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