MolNFT v1 · #154911 · protein + DNA + RNA
Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 4 nt
6KQL · DNA-directed RNA polymerase subunit alpha: “Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 4 nt”. X-ray diffraction, 2 ligands (MG, ZN), 20 pockets (best druggability 0.86). MolNFT…
- PDB
- 6KQL
- Type
- protein + DNA + RNA
- Length
- 3,541 residues
- Chains
- 9
- 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
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 20% helix, 41% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 22% helix, 40% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 29% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1486 | 37% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 47% helix, 12% strand | Q8RQE7 |
| F | RNA polymerase sigma factor siga | protein | 346 | 70% helix, 1% strand | Q5SKW1 |
| G | DNA (5'- D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') | dna | 17 | — | — |
| H | 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*G*)-3') | dna | 24 | — | — |
| I | RNA (5'-R(*(UTP))-R(P*CP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains D, I, B, F
- ZN · Zinc ion · metal · 2 copies · chains D
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 | 781 | 0.86 | 0.89 | 89 | empty |
| 2 | 1073 | 0.86 | 0.87 | 110 | empty |
| 3 | 1066 | 0.85 | 0.86 | 101 | empty |
| 4 | 706 | 0.82 | 0.86 | 68 | empty |
| 5 | 612 | 0.80 | 0.85 | 60 | empty |
Interfaces
22 interfaces between chains.
- C–D · 8921 Ų buried · 127 hydrogen bonds · protein-protein
- D–F · 4080 Ų buried · 48 hydrogen bonds · protein-protein
- C–F · 2480 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 2385 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2081 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6KQL · Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate… · the same entry in another collection · chain I against I, TM-score 1.00
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 6KQL · PDBe 6KQL · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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