Research workbench
Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt
Analyse Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KQD
- Type
- protein + DNA + RNA
- Length
- 7,060 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- DGP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 3.3 · 11 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 21% helix, 43% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 23% helix, 43% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 29% helix, 27% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1486 | 36% helix, 24% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 51% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor SigA | protein | 346 | 68% helix, 1% strand | Q5SKW1 |
| G, Q | DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3') | dna | 16 | — | — |
| H, R | DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3') | dna | 24 | — | — |
| I, S | RNA (5'-R(*GP*GP*A)-3') | rna | 3 | — | — |
| L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 22% helix, 42% strand | Q5SHR6 |
| P | RNA polymerase sigma factor SigA | protein | 347 | 67% helix, 1% strand | Q5SKW1 |
Ligands and binding sites
- DGP · 2'-deoxyguanosine-5'-monophosphate · ligand · 2 copies · chains C, F, G, M, P, Q
- MG · Magnesium ion · metal · 7 copies · chains B, D, I, F, K, N, S, L
- ZN · Zinc ion · metal · 4 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 | 1128 | 0.86 | 0.87 | 106 | MG |
| 2 | 925 | 0.85 | 0.87 | 93 | empty |
| 3 | 1048 | 0.85 | 0.86 | 91 | empty |
| 4 | 1022 | 0.85 | 0.86 | 93 | empty |
| 5 | 636 | 0.84 | 0.89 | 74 | empty |
Interfaces
45 interfaces between chains.
- M–N · 9072 Ų buried · 132 hydrogen bonds · protein-protein
- C–D · 9012 Ų buried · 132 hydrogen bonds · protein-protein
- N–P · 4133 Ų buried · 51 hydrogen bonds · protein-protein
- D–F · 4050 Ų buried · 49 hydrogen bonds · protein-protein
- M–P · 2604 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6KQD · Thermus thermophilus initial transcription complex comprising sigma a and 5'-oh RNA of 3… · the same entry in another collection · chain K against K, 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 6KQD · PDBe 6KQD · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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