MolNFT v1 · #61246 · protein + DNA

Opposite gata DNA binding

3DFX · DNA (5'- D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*…: “Opposite gata DNA binding”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.55). MolNFT v1 #61246 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3DFX
Type: protein + DNA
Length: 156 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DA…
UniProt: P23772
Ligands: ZN
Pockets: 6 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	DNA (5'- D(DTPDTPDGPDAPDTPDAPDAPDAPDTPDCPDAPDGPDAPDGPDAPDTPDA PDAPDCPDC)-3')	dna	20	—	—
Y	DNA (5'- D(DAPDAPDGPDGPDTPDTPDAPDTPDCPDTPDCPDTPDGPDAPDTPDTPDT PDAPDTPDC)-3')	dna	20	—	—
A, B	Trans-acting T-cell-specific transcription factor gata-3	protein	58	22% helix, 0% strand	P23772

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	352	0.55	0.74	29	empty
2	192	0.54	0.79	26	empty
3	148	0.52	0.80	25	empty
4	167	0.50	0.78	24	empty
5	117	0.46	0.78	23	empty

Interfaces

5 interfaces between chains.

X–Y · 794 Å² buried · 68 hydrogen bonds · nucleic-nucleic
X–A · 582 Å² buried · 13 hydrogen bonds · protein-nucleic
Y–B · 553 Å² buried · 14 hydrogen bonds · protein-nucleic
X–B · 427 Å² buried · 10 hydrogen bonds · protein-nucleic
Y–A · 378 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

3DFX · Opposite GATA DNA binding · the same entry in another collection · chain X against X, 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 B against A, TM-score 0.95

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 3DFX · PDBe 3DFX · UniProt P23772

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