MolNFT v1 · #190456 · protein + DNA
Cryo-EM structure of streptomyces coelicolor rnap-promoter open complex with three zur dimers
7X75 · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of streptomyces coelicolor rnap-promoter open complex with three zur dimers”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 7X75
- Type
- protein + DNA
- Length
- 4,223 residues
- Chains
- 15
- 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 0.84
Structure
electron microscopy · 10 distinct chains · 38% helix, 19% 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, 37% strand | A0A6G2M9E1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 23% helix, 36% strand | A0A6G2M9E1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1116 | 27% helix, 25% 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 | 49% helix, 6% strand | Q9KXS1 |
| F | RNA polymerase principal sigma factor hrdb | protein | 301 | 67% helix, 1% strand | P18183 |
| G, H, K, L, M, N | Putative metal uptake regulation protein | protein | 131 | 41% helix, 21% strand | Q9L2H5 |
| O | DNA (84-mer) | dna | 84 | — | — |
| S | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 57 | 67% helix, 4% strand | A0A6G2M9E1 |
| P | DNA (84-mer) | dna | 84 | — | — |
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 | 1029 | 0.84 | 0.85 | 122 | empty |
| 2 | 553 | 0.80 | 0.86 | 53 | empty |
| 3 | 1100 | 0.79 | 0.81 | 91 | empty |
| 4 | 464 | 0.78 | 0.86 | 72 | empty |
| 5 | 286 | 0.77 | 0.89 | 52 | empty |
Interfaces
35 interfaces between chains.
- C–D · 8341 Ų buried · 106 hydrogen bonds · protein-protein
- O–P · 3268 Ų buried · 313 hydrogen bonds · nucleic-nucleic
- D–F · 2664 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2420 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 2065 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7X75 · Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur… · the same entry in another collection · chain P against P, 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 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 7X75 · PDBe 7X75 · UniProt A0A6G2M9E1 · UniProt Q9L0L0 · UniProt Q8CJT1 · UniProt Q9KXS1 · UniProt P18183 · UniProt Q9L2H5
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