MolNFT v1 · #92423 · protein + DNA + RNA
Crystal structure of thermus thermophilus transcription initiation complex containing 2 nt of RNA
4G7O · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus transcription initiation complex containing 2 nt of RNA”. X-ray diffraction, 2 ligands (MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 4G7O
- Type
- protein + DNA + RNA
- Length
- 7,057 residues
- Chains
- 18
- 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 · 12 distinct chains · 37% 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, 39% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 22% 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 | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1482 | 37% helix, 24% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 48% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor | protein | 346 | 67% helix, 2% strand | Q5SKW1 |
| G, Q | 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 | 16 | — | — |
| H, R | 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 | 5'-R(*GP*A)-3' | rna | 2 | — | — |
| L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 22% helix, 43% strand | Q5SHR6 |
| N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1489 | 36% helix, 24% strand | Q8RQE8 |
| P | RNA polymerase sigma factor | protein | 347 | 67% helix, 2% strand | Q5SKW1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains D, I, B, 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 | 1117 | 0.86 | 0.87 | 109 | empty |
| 2 | 1100 | 0.86 | 0.87 | 103 | empty |
| 3 | 603 | 0.85 | 0.90 | 72 | empty |
| 4 | 449 | 0.84 | 0.92 | 53 | empty |
| 5 | 1155 | 0.84 | 0.85 | 93 | empty |
Interfaces
43 interfaces between chains.
- C–D · 8956 Ų buried · 127 hydrogen bonds · protein-protein
- M–N · 8947 Ų buried · 126 hydrogen bonds · protein-protein
- N–P · 4187 Ų buried · 56 hydrogen bonds · protein-protein
- D–F · 4121 Ų buried · 59 hydrogen bonds · protein-protein
- M–P · 2614 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4G7O · Crystal structure of Thermus thermophilus transcription initiation complex containing 2… · the same entry in another collection · chain R against R, 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 4G7O · PDBe 4G7O · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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