Research workbench
Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin
Analyse Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A6H
- Type
- protein
- Length
- 6,796 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 0.86
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 17% 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 | 21% helix, 39% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 25% helix, 22% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1381 | 38% helix, 14% strand | Q8RQE8 |
| E, O | RNA polymerase omega chain | protein | 95 | 46% helix, 3% strand | Q8RQE7 |
| F, P | RNA polymerase sigma factor rpod | protein | 345 | 69% 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 | 1127 | 0.86 | 0.87 | 122 | empty |
| 2 | 894 | 0.85 | 0.87 | 89 | empty |
| 3 | 871 | 0.85 | 0.87 | 90 | empty |
| 4 | 565 | 0.84 | 0.89 | 62 | empty |
| 5 | 1189 | 0.84 | 0.85 | 95 | empty |
Interfaces
19 interfaces between chains.
- C–D · 9360 Ų buried · 123 hydrogen bonds · protein-protein
- M–N · 8831 Ų buried · 111 hydrogen bonds · protein-protein
- N–P · 4235 Ų buried · 48 hydrogen bonds · protein-protein
- D–F · 3865 Ų buried · 63 hydrogen bonds · protein-protein
- N–O · 2506 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2A6H · Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with… · the same entry in another collection · chain P against P, 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 2A6H · PDBe 2A6H · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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