MolNFT v1 · #187866 · protein + DNA
Cryo-EM structure of 27A bound to E. COLI rnap and RRNBP1 promoter complex
7SZK · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of 27A bound to E. COLI rnap and RRNBP1 promoter complex”. Electron microscopy, 3 ligands (D9X, ZN, MG), 20 pockets (best druggability 0.82). MolNFT v1 #187866 on…
- PDB
- 7SZK
- Type
- protein + DNA
- Length
- 3,719 residues
- Chains
- 8
- 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579
- Ligands
- D9X, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 23% helix, 34% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 23% helix, 35% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 32% helix, 21% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1340 | 37% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 59% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 466 | 71% helix, 3% strand | P00579 |
| X | DNA (5'- D(P*CP*TP*CP*GP*TP*AP*GP*AP*GP*TP*CP*CP*GP*TP*GP*TP*CP*A)-3') | dna | 18 | — | — |
| Y | DNA (5'- D(P*CP*TP*CP*GP*TP*AP*GP*AP*GP*TP*CP*CP*GP*TP*GP*TP*CP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
- D9X · (2s,7r,7ar,13ap,16z,18e,20s,21s,22r,23r,24r,25s,26r, 27S,28E)-5,21,23-trihydroxy-27-methoxy-2,4,16,20,22, 24,26-heptamethyl-10-[4-(2-methylpropyl)piperazin-1-yl]-12-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1, 6,15-trioxo-1,2,7,7A-tetrahydro-6H-2,7-(epoxypentadeca[1,11,13]trienoimino)[1]benzofuro[4,5-a]phenoxazin-25-yl acetate · ligand · chains C
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 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 | 576 | 0.82 | 0.87 | 69 | empty |
| 2 | 815 | 0.81 | 0.84 | 75 | empty |
| 3 | 991 | 0.80 | 0.82 | 82 | empty |
| 4 | 797 | 0.77 | 0.81 | 71 | empty |
| 5 | 848 | 0.76 | 0.80 | 92 | empty |
Interfaces
14 interfaces between chains.
- C–D · 8112 Ų buried · 74 hydrogen bonds · protein-protein
- D–F · 2423 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2096 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 1897 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1621 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7SZK · Cryo-EM structure of 27a bound to E. coli RNAP and rrnBP1 promoter complex · the same entry in another collection · chain A against A, 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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 7SZK · PDBe 7SZK · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.