MolNFT v1 · #189754 · protein + DNA
Structure of nf-kb P52 homodimer bound to A/T-centric P-selectin kb DNA fragment
7VUQ · Nuclear factor nf-kappa-B P52 subunit: “Structure of nf-kb P52 homodimer bound to A/T-centric P-selectin kb DNA fragment”. X-ray diffraction, 7 pockets (best druggability 0.82). MolNFT v1 #189754 on GenesisL1: 3D structure, binding…
- PDB
- 7VUQ
- Type
- protein + DNA
- Length
- 627 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
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Nuclear factor nf-kappa-B P52 subunit | protein | 296 | 11% helix, 34% strand | Q00653 |
| D | DNA (5'- D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*AP*AP*CP*CP*CP*CP*TP*TP*G)-3') | dna | 18 | — | — |
| C | DNA (5'- D(*CP*AP*AP*GP*GP*GP*GP*TP*TP*AP*CP*CP*CP*CP*CP*TP*T)-3') | dna | 17 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.82 | 0.83 | 89 | empty |
| 2 | 149 | 0.54 | 0.81 | 30 | empty |
| 3 | 157 | 0.53 | 0.80 | 24 | empty |
| 4 | 196 | 0.49 | 0.76 | 36 | empty |
| 5 | 252 | 0.47 | 0.74 | 27 | empty |
Interfaces
6 interfaces between chains.
- D–C · 760 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- B–A · 734 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–D · 490 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–A · 369 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7VUQ · Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.89
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 7VUQ · PDBe 7VUQ · UniProt Q00653
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