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Hmg-D complexed to a bulge DNA

Analyse Hmg-D complexed to a bulge DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E7J
Type: protein + DNA
Length: 100 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: High mobility group protein D; DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*C)-3')…
UniProt: Q05783
Pockets: 2 · best druggability 0.49

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	High mobility group protein D	protein	74	69% helix, 0% strand	Q05783
B	DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3')	dna	14	—	—
C	DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3')	dna	12	—	—

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.49	0.80	14	empty
2	155	0.41	0.74	12	empty

Interfaces

3 interfaces between chains.

B–C · 612 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–B · 376 Å² buried · 2 hydrogen bonds · protein-nucleic
A–C · 346 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

Q05783 · AlphaFold monomer V2.0 prediction for high mobility group protein D (Q05783) · a predicted model of the same protein · chain A against A, TM-score 0.70

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 Q05783
Elsewhere: RCSB PDB 1E7J · PDBe 1E7J · UniProt Q05783

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