Research workbench

T domain from xenopus laevis bound to DNA

Analyse T domain from xenopus laevis bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XBR
Type: protein + DNA
Length: 415 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP*…
UniProt: P24781
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'- D(APAPTPTPTPCPAPCPAPCPCPTPAPGPGPTPG PTPGPAPAPAP* TP*T)-3')	dna	24	—	—
A	Protein (T protein)	protein	184	22% helix, 36% strand	P24781
B	Protein (T protein)	protein	183	22% helix, 35% strand	P24781

Pockets

5 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	268	0.61	0.80	36	empty
2	263	0.60	0.80	33	empty
3	96	0.36	0.75	13	empty
4	51	0.28	0.76	16	empty
5	52	0.22	0.72	12	empty

Interfaces

6 interfaces between chains.

C–D · 1056 Å² buried · 105 hydrogen bonds · nucleic-nucleic
C–A · 603 Å² buried · 9 hydrogen bonds · protein-nucleic
D–B · 599 Å² buried · 8 hydrogen bonds · protein-nucleic
D–A · 512 Å² buried · 8 hydrogen bonds · protein-nucleic
C–B · 510 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

1XBR · T domain from xenopus laevis bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
P24781 · AlphaFold monomer V2.0 prediction for T-box transcription factor T (P24781) · a predicted model of the same protein · chain A 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 P24781
Elsewhere: RCSB PDB 1XBR · PDBe 1XBR · UniProt P24781

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