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NMR solution structure of the bicoid homeodomain bound to the consensus DNA binding site taatcc

Analyse NMR solution structure of the bicoid homeodomain bound to the consensus DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZQ3
Type: protein + DNA
Length: 94 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'…
UniProt: Q9UAM0
Pockets: 3 · best druggability 0.49

Structure

solution nmr · 3 distinct chains · 62% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(GPCPTPCPTPAPAPTPCPCPCPCP*G)-3'	dna	13	—	—
B	5'-D(CPGPGPGPGPAPTPTPAPGPAPGP*C)-3'	dna	13	—	—
P	Homeotic bicoid protein	protein	68	62% helix, 0% strand	Q9UAM0

Pockets

3 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	173	0.49	0.77	23	empty
2	67	0.41	0.81	14	empty
3	69	0.31	0.74	12	empty

Interfaces

3 interfaces between chains.

B–P · 655 Å² buried · 19 hydrogen bonds · protein-nucleic
A–B · 586 Å² buried · 60 hydrogen bonds · nucleic-nucleic
A–P · 462 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

1ZQ3 · NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site… · the same entry in another collection · chain A against A, 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 Q9UAM0
Elsewhere: RCSB PDB 1ZQ3 · PDBe 1ZQ3 · UniProt Q9UAM0

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