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Adjacent gata DNA binding

Analyse Adjacent gata DNA binding in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DFV
Type: protein + DNA
Length: 152 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*DTP*DTP*DAP*DTP*DC…
UniProt: P23772
Ligands: ZN
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Y	DNA (5'- D(DTPDTPDCPDTPDGPDAPDTPDAPDAPDGPDAPDCPDTPDTPDAPDTPDC PDTPDGPDC)-3')	dna	20	—	—
Z	DNA (5'- D(DAPDAPDGPDCPDAPDGPDAPDTPDAPDAPDGPDTPDCPDTPDTPDAPDT PDCPDAPDG)-3')	dna	20	—	—
D, C	Trans-acting T-cell-specific transcription factor gata-3	protein	56	23% helix, 11% strand	P23772

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains D, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.78	0.88	53	empty
2	58	0.44	0.83	16	empty
3	57	0.40	0.81	17	empty
4	68	0.28	0.73	12	empty

Interfaces

6 interfaces between chains.

Y–Z · 801 Å² buried · 64 hydrogen bonds · nucleic-nucleic
Z–C · 631 Å² buried · 12 hydrogen bonds · protein-nucleic
Y–D · 625 Å² buried · 14 hydrogen bonds · protein-nucleic
Y–C · 588 Å² buried · 9 hydrogen bonds · protein-nucleic
Z–D · 579 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3DFV · Adjacent GATA DNA binding · the same entry in another collection · chain Y against Y, TM-score 1.00
P23772 · AlphaFold monomer V2.0 prediction for trans-acting T-cell-specific transcription factor… · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P23772
Elsewhere: RCSB PDB 3DFV · PDBe 3DFV · UniProt P23772

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