MolNFT v1 · #189753 · protein + DNA
Structure of nf-kb P52 homodimer bound to +1/-1 swap P-selectin kb DNA fragment
7VUP · Nuclear factor nf-kappa-B P52 subunit: “Structure of nf-kb P52 homodimer bound to +1/-1 swap P-selectin kb DNA fragment”. X-ray diffraction, 11 pockets (best druggability 0.81). MolNFT v1 #189753 on GenesisL1: 3D structure, binding…
- PDB
- 7VUP
- Type
- protein + DNA
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear factor nf-kappa-B P52 subunit; DNA (5'…
- UniProt
- Q00653
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear factor nf-kappa-B P52 subunit | protein | 296 | 10% helix, 34% strand | Q00653 |
| C | DNA (5'- D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3') | dna | 17 | — | — |
| D | DNA (5'- D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3') | dna | 17 | — | — |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.81 | 0.83 | 73 | empty |
| 2 | 121 | 0.57 | 0.84 | 30 | empty |
| 3 | 102 | 0.48 | 0.81 | 19 | empty |
| 4 | 109 | 0.46 | 0.79 | 20 | empty |
| 5 | 54 | 0.39 | 0.81 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 767 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–B · 720 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 530 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 363 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7VUP · Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q00653 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P100 subunit (Q00653) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q00653
- Elsewhere: RCSB PDB 7VUP · PDBe 7VUP · UniProt Q00653
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