GL1X · GenesisL1 explorer

Research workbench

Solution structure of the non-sequence-specific hmgb protein NHP6A in complex with sry DNA

Analyse Solution structure of the non-sequence-specific hmgb protein NHP6A in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1J5N
Type
protein + DNA
Length
123 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'…
UniProt
P11632
Pockets
3 · best druggability 0.59

Structure

solution nmr · 3 distinct chains · 65% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'dna15——
C5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'dna15——
ANonhistone chromosomal protein 6Aprotein9365% helix, 0% strandP11632

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13120.590.7822empty
21550.560.8220empty
3690.350.7712empty

Interfaces

3 interfaces between chains.

  • B–A · 1020 Ų buried · 10 hydrogen bonds · protein-nucleic
  • C–A · 918 Ų buried · 16 hydrogen bonds · protein-nucleic
  • B–C · 660 Ų buried · 65 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1J5N · Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA · the same entry in another collection · chain B against B, TM-score 1.00
  • P11632 · AlphaFold monomer V2.0 prediction for non-histone chromosomal protein 6A (P11632) · a predicted model of the same protein · chain A against A, TM-score 0.63

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.