MolNFT v1 · #11199 · protein + DNA
Crystal structure of the NC2-tbp-DNA ternary complex
1JFI · 5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP…: “Crystal structure of the NC2-tbp-DNA ternary complex”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #11199 on GenesisL1: 3D structure, binding sites…
- PDB
- 1JFI
- Type
- protein + DNA
- Length
- 417 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP *C)-3'…
- UniProt
- Q14919, Q01658, P20226
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP *C)-3' | dna | 18 | — | — |
| E | 5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP* a)-3' | dna | 18 | — | — |
| A | Transcription regulator NC2 alpha chain | protein | 63 | 60% helix, 3% strand | Q14919 |
| B | Transcription regulator NC2 beta chain | protein | 135 | 80% helix, 1% strand | Q01658 |
| C | Tata-box-binding protein (tbp) | protein | 183 | 27% helix, 36% strand | P20226 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.73 | 0.77 | 67 | empty |
| 2 | 236 | 0.49 | 0.75 | 27 | empty |
| 3 | 122 | 0.41 | 0.76 | 21 | empty |
| 4 | 65 | 0.36 | 0.77 | 12 | empty |
| 5 | 73 | 0.34 | 0.76 | 14 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2046 Ų buried · 9 hydrogen bonds · protein-protein
- D–C · 785 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–C · 768 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 762 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 758 Ų buried · 68 hydrogen bonds · nucleic-nucleic
Compared structures
- 1JFI · Crystal Structure of the NC2-TBP-DNA Ternary Complex · the same entry in another collection · chain C against C, TM-score 1.00
- P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q14919 · AlphaFold monomer V2.0 prediction for DR1-associated corepressor (Q14919) · a predicted model of the same protein · chain A against A, TM-score 0.90
- Q01658 · AlphaFold monomer V2.0 prediction for protein DR1 (Q01658) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 Q14919
- Every structure of UniProt Q01658
- Every structure of UniProt P20226
- Elsewhere: RCSB PDB 1JFI · PDBe 1JFI · UniProt Q14919 · UniProt Q01658 · UniProt P20226
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.