Research workbench

NKX2.5 homeodomain dimer bound to anf-242 DNA

Analyse NKX2.5 homeodomain dimer bound to anf-242 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RKQ
Type: protein + DNA
Length: 153 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homeobox protein nkx-2.5; Anf-242 DNA
UniProt: P52952
Ligands: MG
Pockets: 4 · best druggability 0.42

Structure

x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homeobox protein nkx-2.5	protein	58	64% helix, 0% strand	P52952
B	Homeobox protein nkx-2.5	protein	57	63% helix, 0% strand	P52952
C	Anf-242 DNA	dna	19	—	—
D	Anf-242 DNA	dna	19	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 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	141	0.42	0.76	13	empty
2	106	0.35	0.74	12	empty
3	83	0.34	0.75	14	empty
4	68	0.31	0.75	15	empty

Interfaces

5 interfaces between chains.

C–D · 863 Å² buried · 90 hydrogen bonds · nucleic-nucleic
A–D · 504 Å² buried · 5 hydrogen bonds · protein-nucleic
B–C · 452 Å² buried · 8 hydrogen bonds · protein-nucleic
A–C · 398 Å² buried · 7 hydrogen bonds · protein-nucleic
B–D · 386 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

3RKQ · NKX2.5 Homeodomain dimer bound to ANF-242 DNA · the same entry in another collection · chain A against A, TM-score 1.00
P52952 · AlphaFold monomer V2.0 prediction for homeobox protein nkx-2.5 (P52952) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P52952
Elsewhere: RCSB PDB 3RKQ · PDBe 3RKQ · UniProt P52952

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