MolNFT v1 · #21350 · protein + DNA + RNA
T7 RNA polymerase alpha beta methylene ATP elongation complex
1S76 · DNA (5'- D(P*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP…: “T7 RNA polymerase alpha beta methylene ATP elongation complex”. X-ray diffraction, 2 ligands (APC, MG), 16 pockets (best druggability 0.78). MolNFT v1 #21350 on…
- PDB
- 1S76
- Type
- protein + DNA + RNA
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*G P*TP*T)-3'); DNA…
- EC
- 2.7.7.6
- UniProt
- P00573
- Ligands
- APC, MG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'- D(P*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*G P*TP*T)-3') | dna | 21 | — | — |
| N | DNA (5'- D(P*TP*TP*TP*AP*CP*GP*TP*TP*GP*CP*GP*CP*AP*CP*GP*GP*C)-3') | dna | 17 | — | — |
| R | RNA (5'-R(P*AP*CP*AP*CP*GP*GP*CP*GP*A)-3') | rna | 9 | — | — |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 829 | 51% helix, 7% strand | P00573 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains T, R, D
- MG · Magnesium ion · metal · 2 copies · chains D, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.78 | 0.83 | 64 | empty |
| 2 | 377 | 0.77 | 0.87 | 41 | empty |
| 3 | 652 | 0.77 | 0.82 | 64 | MG, APC |
| 4 | 533 | 0.73 | 0.81 | 61 | empty |
| 5 | 531 | 0.71 | 0.81 | 42 | empty |
Interfaces
5 interfaces between chains.
- T–D · 1318 Ų buried · 17 hydrogen bonds · protein-nucleic
- N–D · 903 Ų buried · 11 hydrogen bonds · protein-nucleic
- R–D · 807 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–N · 496 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- T–R · 358 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 1S76 · T7 RNA polymerase alpha beta methylene ATP elongation complex · the same entry in another collection · chain T against T, 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 P00573
- Elsewhere: RCSB PDB 1S76 · PDBe 1S76 · UniProt P00573
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.