MolNFT v1 · #145667 · protein + DNA
Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic kanglemycin a
6CUU · DNA-directed RNA polymerase subunit alpha: “Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic kanglemycin a”. X-ray diffraction, 3 ligands (KNG, ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6CUU
- Type
- protein + DNA
- Length
- 3,526 residues
- Chains
- 8
- 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
- Q72I32, Q72HM5, Q72HM6, Q72ID6, Q72L95
- Ligands
- KNG, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 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 | 227 | 22% helix, 38% strand | Q72I32 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 21% helix, 43% strand | Q72I32 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 30% helix, 27% strand | Q72HM5 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1485 | 37% helix, 24% strand | Q72HM6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 48% helix, 11% strand | Q72ID6 |
| F | RNA polymerase sigma factor siga | protein | 346 | 69% helix, 1% strand | Q72L95 |
| G | DNA (5'- D(P*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') | dna | 17 | — | — |
| H | DNA (5'- D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*CP*TP*CP*TP*GP*AP*TP*GP*CP*A)- 3') | dna | 22 | — | — |
Ligands and binding sites
- KNG · Kanglemycin A · ligand · chains C, F
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 2 copies · chains D, B
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 | 1080 | 0.86 | 0.87 | 94 | empty |
| 2 | 413 | 0.85 | 0.93 | 56 | empty |
| 3 | 1086 | 0.85 | 0.86 | 102 | empty |
| 4 | 649 | 0.80 | 0.85 | 60 | empty |
| 5 | 523 | 0.79 | 0.86 | 63 | empty |
Interfaces
18 interfaces between chains.
- C–D · 8834 Ų buried · 133 hydrogen bonds · protein-protein
- D–F · 3939 Ų buried · 59 hydrogen bonds · protein-protein
- D–E · 2354 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 2328 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 2099 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6CUU · Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic… · the same entry in another collection · chain H against H, TM-score 1.00
- Q72HM5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q72HM5) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q72HM6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q72HM6) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q72ID6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q72ID6) · a predicted model of the same protein · chain E against A, TM-score 0.97
- Q72I32 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q72I32) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q72I32
- Every structure of UniProt Q72HM5
- Every structure of UniProt Q72HM6
- Every structure of UniProt Q72ID6
- Every structure of UniProt Q72L95
- Elsewhere: RCSB PDB 6CUU · PDBe 6CUU · UniProt Q72I32 · UniProt Q72HM5 · UniProt Q72HM6 · UniProt Q72ID6 · UniProt Q72L95
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