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Structure of LHX4 transcription factor complexed with DNA

Analyse Structure of LHX4 transcription factor complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HOD
Type: protein + DNA
Length: 159 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LIM/HOMEOBOX protein LHX4; DNA (5'- D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP…
UniProt: Q969G2
Pockets: 5 · best druggability 0.55

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LIM/HOMEOBOX protein LHX4	protein	61	66% helix, 0% strand	Q969G2
B	DNA (5'- D(PAPCPCPTPAPAPTPTPAPGPGPCPGPTPAPAPTPTPAPG)-3')	dna	20	—	—
C	DNA (5'- D(PCPTPAPAPTPTPAPCPGPCPCPTPAPAPTPTPAPGPGPT)-3')	dna	20	—	—
D	LIM/HOMEOBOX protein LHX4	protein	58	66% helix, 0% strand	Q969G2

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	178	0.55	0.80	23	empty
2	224	0.53	0.77	25	empty
3	64	0.38	0.80	11	empty
4	64	0.30	0.75	12	empty
5	54	0.27	0.74	14	empty

Interfaces

5 interfaces between chains.

B–C · 870 Å² buried · 74 hydrogen bonds · nucleic-nucleic
B–D · 501 Å² buried · 11 hydrogen bonds · protein-nucleic
C–D · 455 Å² buried · 11 hydrogen bonds · protein-nucleic
A–B · 442 Å² buried · 10 hydrogen bonds · protein-nucleic
A–C · 422 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

5HOD · Structure of LHX4 transcription factor complexed with DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q969G2 · AlphaFold monomer V2.0 prediction for LIM/HOMEOBOX protein LHX4 (Q969G2) · a predicted model of the same protein · chain D against A, TM-score 0.92

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 Q969G2
Elsewhere: RCSB PDB 5HOD · PDBe 5HOD · UniProt Q969G2

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