MolNFT v1 · #189665 · protein + DNA + RNA
Cryo-EM structure of streptomyces coelicolor transcription initial complex with one zur dimer
7VPZ · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of streptomyces coelicolor transcription initial complex with one zur dimer”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 7VPZ
- Type
- protein + DNA + RNA
- Length
- 3,647 residues
- Chains
- 11
- Method
- electron microscopy
- 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
- A0A6G2M9E1, Q9L0L0, Q8CJT1, Q9KXS1, P18183, Q9L2H5
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 19% helix, 35% strand | A0A6G2M9E1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 22% helix, 38% strand | A0A6G2M9E1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1116 | 27% helix, 24% strand | Q9L0L0 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1259 | 44% helix, 12% strand | Q8CJT1 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 77 | 48% helix, 4% strand | Q9KXS1 |
| F | RNA polymerase principal sigma factor hrdb | protein | 301 | 66% helix, 2% strand | P18183 |
| M, N | Putative metal uptake regulation protein | protein | 131 | 42% helix, 18% strand | Q9L2H5 |
| O | DNA (84-mer) | dna | 84 | — | — |
| P | DNA (84-mer) | dna | 84 | — | — |
| Q | RNA | rna | 5 | — | — |
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 | 475 | 0.85 | 0.92 | 70 | empty |
| 2 | 1156 | 0.83 | 0.84 | 124 | empty |
| 3 | 889 | 0.81 | 0.83 | 73 | empty |
| 4 | 707 | 0.81 | 0.86 | 82 | empty |
| 5 | 149 | 0.78 | 0.95 | 17 | empty |
Interfaces
25 interfaces between chains.
- C–D · 8357 Ų buried · 111 hydrogen bonds · protein-protein
- O–P · 3307 Ų buried · 323 hydrogen bonds · nucleic-nucleic
- D–F · 2635 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2347 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 2080 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7VPZ · Cryo-EM structure of Streptomyces coelicolor transcription initial complex with one Zur… · the same entry in another collection · chain P against P, TM-score 1.00
- Q9L0L0 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q9L0L0) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A0A6G2M9E1
- Every structure of UniProt Q9L0L0
- Every structure of UniProt Q8CJT1
- Every structure of UniProt Q9KXS1
- Every structure of UniProt P18183
- Every structure of UniProt Q9L2H5
- Elsewhere: RCSB PDB 7VPZ · PDBe 7VPZ · UniProt A0A6G2M9E1 · UniProt Q9L0L0 · UniProt Q8CJT1 · UniProt Q9KXS1 · UniProt P18183 · UniProt Q9L2H5
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