Research workbench

Antennapedia homeodomain-DNA complex

Analyse Antennapedia homeodomain-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 9ANT
Type: protein + DNA
Length: 172 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)- 3'); DNA…
UniProt: P02833
Ligands: NI
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E	DNA (5'-D(APGPAPAPAPGPCPCPAPTPTPAPGPAP*G)- 3')	dna	15	—	—
D, F	DNA (5'-D(TPCPTPCPTPAPAPTPGPGPCPTPTPTP*C)- 3')	dna	15	—	—
A, B	Antennapedia homeodomain	protein	56	70% helix, 0% strand	P02833

Ligands and binding sites

NI · Nickel (II) ion · metal · chains B

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

Pockets

3 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	221	0.56	0.79	28	empty
2	227	0.55	0.78	27	empty
3	50	0.27	0.75	12	empty

Interfaces

6 interfaces between chains.

C–D · 636 Å² buried · 62 hydrogen bonds · nucleic-nucleic
E–F · 633 Å² buried · 59 hydrogen bonds · nucleic-nucleic
C–A · 558 Å² buried · 6 hydrogen bonds · protein-nucleic
E–B · 509 Å² buried · 6 hydrogen bonds · protein-nucleic
F–B · 430 Å² buried · 15 hydrogen bonds · protein-nucleic

Compared structures

9ANT · Antennapedia homeodomain-DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
P02833 · AlphaFold monomer V2.0 prediction for homeotic protein antennapedia (P02833) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P02833
Elsewhere: RCSB PDB 9ANT · PDBe 9ANT · UniProt P02833

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