MolNFT v1 · #21351 · protein + DNA + RNA
T7 rnap product pyrophosphate elongation complex
1S77 · DNA (5'- D(*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*…: “T7 rnap product pyrophosphate elongation complex”. X-ray diffraction, 2 ligands (POP, MG), 15 pockets (best druggability 0.80). MolNFT v1 #21351 on GenesisL1: 3D…
- PDB
- 1S77
- 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(*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*GP *TP*T)-3'); DNA (5'…
- EC
- 2.7.7.6
- UniProt
- P00573
- Ligands
- POP, MG
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'- D(*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*GP *TP*T)-3') | dna | 21 | — | — |
| N | DNA (5'- D(*TP*TP*TP*AP*CP*GP*TP*TP*GP*CP*GP*CP*AP*CP*GP*GP*C)-3') | dna | 17 | — | — |
| R | RNA (5'-R(*AP*CP*AP*CP*GP*GP*CP*GP*AP*(3DA))-3') | rna | 10 | — | — |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 828 | 52% helix, 8% strand | P00573 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.80 | 0.84 | 85 | empty |
| 2 | 326 | 0.79 | 0.90 | 38 | empty |
| 3 | 395 | 0.74 | 0.84 | 50 | MG, POP |
| 4 | 555 | 0.72 | 0.81 | 47 | empty |
| 5 | 182 | 0.67 | 0.87 | 27 | empty |
Interfaces
5 interfaces between chains.
- T–D · 1301 Ų buried · 17 hydrogen bonds · protein-nucleic
- R–D · 996 Ų buried · 24 hydrogen bonds · protein-nucleic
- N–D · 835 Ų buried · 7 hydrogen bonds · protein-nucleic
- T–N · 506 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- T–R · 426 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1S77 · T7 RNAP product pyrophosphate 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 1S77 · PDBe 1S77 · UniProt P00573
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