MolNFT v1 · #166060 · protein + DNA

Structure of tbp bound to C-C mismatch containing tata site

6UEQ · Tata-box-binding protein 1: “Structure of tbp bound to C-C mismatch containing tata site”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.40). MolNFT v1 #166060 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6UEQ
Type: protein + DNA
Length: 215 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tata-box-binding protein 1; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*CP*GP*GP*CP*A)-3'); DNA…
UniProt: P28147
Ligands: SO4
Pockets: 1 · best druggability 0.40

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Tata-box-binding protein 1	protein	187	26% helix, 35% strand	P28147
C	DNA (5'-D(GPCPTPAPTPAPAPAPAPCPGPGPCPA)-3')	dna	14	—	—
D	DNA (5'-D(TPGPCPCPCPTPTPTPTPAPTPAPGPC)-3')	dna	14	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	185	0.40	0.72	22	SO4

Interfaces

3 interfaces between chains.

B–D · 856 Å² buried · 10 hydrogen bonds · protein-nucleic
B–C · 837 Å² buried · 6 hydrogen bonds · protein-nucleic
C–D · 616 Å² buried · 58 hydrogen bonds · nucleic-nucleic

Compared structures

6UEQ · Structure of TBP bound to C-C mismatch containing TATA site · 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 6UEQ · PDBe 6UEQ · UniProt P28147

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