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Structure of TBP-Hoogsteen containing DNA complex

Analyse Structure of TBP-Hoogsteen containing DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NJQ
Type: protein + DNA
Length: 430 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.75
Source: Arabidopsis thaliana; SYNTHETIC CONSTRUCT
Molecule: TATA-box-binding protein 1; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3'); DNA…
UniProt: P28147
Pockets: 3 · best druggability 0.39

Structure

x-ray diffraction · resolution 2.75 · 3 distinct chains · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	TATA-box-binding protein 1	protein	187	26% helix, 35% strand	P28147
E, C	DNA (5'-D(GPCPTPAPTPAPAPAPCPGPGPGPCPA)-3')	dna	14	—	—
F, D	DNA (5'-D(TPGPCPCPCPGPTPTPTPAPTPAPGPC)-3')	dna	14	—	—

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	165	0.39	0.72	16	empty
2	148	0.37	0.73	18	empty
3	56	0.31	0.76	15	empty

Interfaces

7 interfaces between chains.

A–D · 826 Å² buried · 9 hydrogen bonds · protein-nucleic
B–E · 819 Å² buried · 9 hydrogen bonds · protein-nucleic
B–F · 816 Å² buried · 9 hydrogen bonds · protein-nucleic
A–C · 792 Å² buried · 5 hydrogen bonds · protein-nucleic
C–D · 623 Å² buried · 62 hydrogen bonds · nucleic-nucleic

Compared structures

6NJQ · Structure of tbp-hoogsteen containing DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
P28147 · AlphaFold monomer V2.0 prediction for tata-box-binding protein 1 (P28147) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P28147
Elsewhere: RCSB PDB 6NJQ · PDBe 6NJQ · UniProt P28147

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