MolNFT v1 · #30275 · protein
Structure of thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin
1ZYR · DNA-directed RNA polymerase alpha chain: “Structure of thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin”. X-ray diffraction, 3 ligands (STD, ZN, MG), 20 pockets (best druggability 0.87).…
- 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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