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Structure of a complex of tandem hmg boxes and DNA

Analyse Structure of a complex of tandem hmg boxes and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GZK
Type: protein + DNA
Length: 191 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP*C)-3'…
UniProt: Q6J4I5, Q548R9
Pockets: 1 · best druggability 0.71

Structure

solution nmr · 3 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(GPGPGPAPTPCPTPAPAPAPCPAPAPTPGPC)-3'	dna	16	—	—
C	5'-D(GPCPAPTPTPGPTPTPTPAPGPAPTPCPCPC)-3'	dna	16	—	—
A	Sex-determining region on Y / HMGB1	protein	159	69% helix, 0% strand	Q6J4I5, Q548R9

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.71	0.92	20	empty

Interfaces

3 interfaces between chains.

B–A · 1546 Å² buried · 33 hydrogen bonds · protein-nucleic
C–A · 1336 Å² buried · 19 hydrogen bonds · protein-nucleic
B–C · 742 Å² buried · 71 hydrogen bonds · nucleic-nucleic

Compared structures

2GZK · Structure of a complex of tandem HMG boxes and DNA · the same entry in another collection · chain B against B, 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 Q6J4I5
Every structure of UniProt Q548R9
Elsewhere: RCSB PDB 2GZK · PDBe 2GZK · UniProt Q6J4I5 · UniProt Q548R9

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