Research workbench
Crystal structure of a higher-order complex of P50:RELA bound to the HIV-1 ltr
Analyse Crystal structure of a higher-order complex of P50:RELA bound to the HIV-1 ltr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GUT
- Type
- protein + DNA
- Length
- 2,444 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor P65; Nuclear factor nf-kappa-B P105 subunit; HIV-ltr core forward…
- UniProt
- Q04206, P19838
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Transcription factor P65 | protein | 273 | 4% helix, 36% strand | Q04206 |
| B, D, F, H | Nuclear factor nf-kappa-B P105 subunit | protein | 312 | 13% helix, 37% strand | P19838 |
| X, I | HIV-ltr core forward strand | dna | 26 | — | — |
| Y, J | HIV-ltr core reverse strand | dna | 26 | — | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.84 | 0.86 | 63 | empty |
| 2 | 1177 | 0.83 | 0.85 | 105 | empty |
| 3 | 831 | 0.83 | 0.86 | 56 | empty |
| 4 | 1179 | 0.82 | 0.83 | 95 | empty |
| 5 | 466 | 0.68 | 0.79 | 37 | empty |
Interfaces
34 interfaces between chains.
- X–Y · 1167 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- I–J · 1155 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- G–H · 762 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 752 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 742 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3GUT · Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR · the same entry in another collection · chain J against J, 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 Q04206
- Every structure of UniProt P19838
- Elsewhere: RCSB PDB 3GUT · PDBe 3GUT · UniProt Q04206 · UniProt P19838
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.