Research workbench
Crystal structure of nfat bound to the HIV-1 ltr tandem kappab enhancer element
Analyse Crystal structure of nfat bound to the HIV-1 ltr tandem kappab enhancer element in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O93
- Type
- protein + DNA
- Length
- 908 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kappab enhancer element, DNA 25-mer; Actor of activated T-cells, cytoplasmic 2
- UniProt
- Q13469
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kappab enhancer element, DNA 25-mer | dna | 25 | — | — |
| B | Kappab enhancer element, DNA 25-mer | dna | 25 | — | — |
| L, O | Actor of activated T-cells, cytoplasmic 2 | protein | 287 | 3% helix, 44% strand | Q13469 |
| M | Actor of activated T-cells, cytoplasmic 2 | protein | 284 | 3% helix, 43% strand | Q13469 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.69 | 0.78 | 59 | empty |
| 2 | 215 | 0.67 | 0.85 | 25 | empty |
| 3 | 392 | 0.63 | 0.78 | 61 | empty |
| 4 | 124 | 0.50 | 0.80 | 17 | empty |
| 5 | 180 | 0.44 | 0.74 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1116 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- L–M · 775 Ų buried · 14 hydrogen bonds · protein-protein
- A–O · 640 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–M · 538 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–M · 532 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 2O93 · Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element · the same entry in another collection · chain B against B, TM-score 1.00
- Q13469 · AlphaFold monomer V2.0 prediction for nuclear factor of activated T-cells, cytoplasmic 2… · a predicted model of the same protein · chain M against A, TM-score 0.84
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 Q13469
- Elsewhere: RCSB PDB 2O93 · PDBe 2O93 · UniProt Q13469
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