Research workbench
F. tularensis RNAPS70-(mgla-sspa)-ppgpp-pigr-igla DNA complex
Analyse F. tularensis RNAPS70-(mgla-sspa)-ppgpp-pigr-igla DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WMT
- Type
- protein + DNA
- Length
- 4,003 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit omega; DNA-directed RNA polymerase subunit alpha 1…
- EC
- 2.7.7.6
- UniProt
- Q2A273, Q2A5E5, Q2A4H7, Q2A1M7, A0A0B6CT24, A0A5Q3U6R7, A0A0B3WH85
- Ligands
- G4P, MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 13 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 69 | 61% helix, 0% strand | Q2A273 |
| A | DNA-directed RNA polymerase subunit alpha 1 (EC 2.7.7.6) | protein | 223 | 22% helix, 30% strand | Q2A5E5 |
| B | DNA-directed RNA polymerase subunit alpha 2 (EC 2.7.7.6) | protein | 230 | 20% helix, 32% strand | Q2A4H7 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1187 | 31% helix, 21% strand | Q2A1M7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1159 | 44% helix, 14% strand | — |
| G | DNA nt-strand | dna | 52 | — | — |
| H | DNA T-strand | dna | 42 | — | — |
| J | DNA T-strand downstream | dna | 11 | — | — |
| K, L | Actds | protein | 73 | 60% helix, 3% strand | — |
| M | Macrophage growth locus, subunit a | protein | 201 | 64% helix, 5% strand | A0A0B6CT24 |
| S | Glutathione S-transferase | protein | 202 | 53% helix, 4% strand | A0A5Q3U6R7 |
| X | DNA nt-strand downstream | dna | 11 | — | — |
| Z | RNA polymerase sigma factor rpod | protein | 470 | 68% helix, 1% strand | A0A0B3WH85 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains E, D, M, S
- MG · Magnesium ion · metal · 2 copies · chains D, S
- 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 | 1148 | 0.84 | 0.85 | 95 | empty |
| 2 | 1168 | 0.82 | 0.83 | 140 | empty |
| 3 | 774 | 0.81 | 0.84 | 59 | empty |
| 4 | 515 | 0.78 | 0.85 | 54 | empty |
| 5 | 439 | 0.78 | 0.86 | 44 | empty |
Interfaces
32 interfaces between chains.
- C–D · 8182 Ų buried · 65 hydrogen bonds · protein-protein
- D–Z · 2432 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1940 Ų buried · 180 hydrogen bonds · nucleic-nucleic
- A–B · 1902 Ų buried · 6 hydrogen bonds · protein-protein
- G–Z · 1738 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 6WMT · F. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex · the same entry in another collection · chain Z against Z, 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 Q2A273
- Every structure of UniProt Q2A5E5
- Every structure of UniProt Q2A4H7
- Every structure of UniProt Q2A1M7
- Every structure of UniProt A0A0B6CT24
- Every structure of UniProt A0A5Q3U6R7
- Every structure of UniProt A0A0B3WH85
- Elsewhere: RCSB PDB 6WMT · PDBe 6WMT · UniProt Q2A273 · UniProt Q2A5E5 · UniProt Q2A4H7 · UniProt Q2A1M7 · UniProt A0A0B6CT24 · UniProt A0A5Q3U6R7 · UniProt A0A0B3WH85
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