MolNFT v1 · #168639 · protein + DNA + RNA
F. tularensis RNAPS70-igla DNA complex
6WMP · DNA-directed RNA polymerase subunit alpha 1: “F. tularensis RNAPS70-igla DNA complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #168639 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WMP
- Type
- protein + DNA + RNA
- Length
- 2,926 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha 1; DNA-directed RNA polymerase subunit alpha 2…
- EC
- 2.7.7.6
- UniProt
- Q2A5E5, Q2A4H7, Q2A1M7, Q2A273
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 28% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha 1 (EC 2.7.7.6) | protein | 225 | 17% helix, 31% strand | Q2A5E5 |
| B | DNA-directed RNA polymerase subunit alpha 2 (EC 2.7.7.6) | protein | 230 | 17% helix, 29% strand | Q2A4H7 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1196 | 25% helix, 20% strand | Q2A1M7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1159 | 35% helix, 13% strand | — |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 69 | 45% helix, 0% strand | Q2A273 |
| F | DNA nt-strand | dna | 13 | — | — |
| G | DNA T-strand | dna | 24 | — | — |
| R | RNA | rna | 10 | — | — |
Ligands and binding sites
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 | 1071 | 0.84 | 0.85 | 86 | empty |
| 2 | 845 | 0.81 | 0.84 | 80 | empty |
| 3 | 886 | 0.80 | 0.83 | 103 | empty |
| 4 | 798 | 0.78 | 0.82 | 65 | empty |
| 5 | 579 | 0.77 | 0.83 | 58 | empty |
Interfaces
16 interfaces between chains.
- C–D · 7915 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 2108 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1612 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1597 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1079 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WMP · F. tularensis RNAPs70-iglA DNA complex · the same entry in another collection · chain R against R, TM-score 1.00
- Q2A1M7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q2A1M7) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q2A5E5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha 1 (Q2A5E5) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q2A4H7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha 2 (Q2A4H7) · a predicted model of the same protein · chain B against A, TM-score 0.90
- Q2A273 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q2A273) · a predicted model of the same protein · chain E against A, TM-score 0.76
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 Q2A5E5
- Every structure of UniProt Q2A4H7
- Every structure of UniProt Q2A1M7
- Every structure of UniProt Q2A273
- Elsewhere: RCSB PDB 6WMP · PDBe 6WMP · UniProt Q2A5E5 · UniProt Q2A4H7 · UniProt Q2A1M7 · UniProt Q2A273
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.