Research workbench
The kb DNA sequence from the hlv-ltr functions as an allosteric regulator of HIV transcription
Analyse The kb DNA sequence from the hlv-ltr functions as an allosteric regulator of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LEI
- Type
- protein + DNA
- Length
- 619 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3'; 5'…
- UniProt
- Q04207, P25799
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3' | dna | 17 | — | — |
| D | 5'- D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP* G)-3' | dna | 17 | — | — |
| A | Nuclear factor nf-kappa-B P65 subunit | protein | 273 | 8% helix, 38% strand | Q04207 |
| B | Nuclear factor nf-kappa-B P50 subunit | protein | 312 | 10% helix, 32% strand | P25799 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.83 | 0.85 | 59 | empty |
| 2 | 317 | 0.51 | 0.74 | 38 | empty |
| 3 | 50 | 0.42 | 0.83 | 15 | empty |
| 4 | 63 | 0.38 | 0.80 | 12 | empty |
| 5 | 75 | 0.37 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 789 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–B · 743 Ų buried · 12 hydrogen bonds · protein-protein
- D–B · 571 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 568 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–A · 305 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
- 1LEI · The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV… · the same entry in another collection · chain C against C, TM-score 1.00
- P25799 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P25799) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q04207
- Every structure of UniProt P25799
- Elsewhere: RCSB PDB 1LEI · PDBe 1LEI · UniProt Q04207 · UniProt P25799
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