MolNFT v1 · #92420 · protein + DNA
Crystal structure of thermus thermophilus transcription initiation complex
4G7H · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus transcription initiation complex”. X-ray diffraction, 2 ligands (MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #92420 on GenesisL1: 3D…
- PDB
- 4G7H
- Type
- protein + DNA
- Length
- 7,054 residues
- Chains
- 16
- 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 0.87
Structure
x-ray diffraction · 10 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, 39% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 21% helix, 41% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 30% helix, 27% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1486 | 37% helix, 24% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 49% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor | protein | 346 | 69% 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* 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 | — | — |
| L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 21% helix, 42% strand | Q5SHR6 |
| P | RNA polymerase sigma factor | protein | 347 | 69% helix, 2% strand | Q5SKW1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains B, D, F, K, N, L, P
- 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 | 1104 | 0.87 | 0.89 | 124 | empty |
| 2 | 990 | 0.86 | 0.87 | 92 | MG |
| 3 | 1048 | 0.85 | 0.86 | 96 | empty |
| 4 | 647 | 0.84 | 0.89 | 75 | empty |
| 5 | 515 | 0.84 | 0.90 | 64 | empty |
Interfaces
38 interfaces between chains.
- M–N · 9047 Ų buried · 125 hydrogen bonds · protein-protein
- C–D · 9005 Ų buried · 126 hydrogen bonds · protein-protein
- N–P · 4109 Ų buried · 52 hydrogen bonds · protein-protein
- D–F · 4049 Ų buried · 56 hydrogen bonds · protein-protein
- M–P · 2645 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4G7H · Crystal structure of Thermus thermophilus transcription initiation complex · 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 4G7H · PDBe 4G7H · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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