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Double stranded DNA binding protein

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

PDB: 3EIK
Type: protein
Length: 357 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tata-box-binding protein
UniProt: Q8ST28
Pockets: 5 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tata-box-binding protein	protein	178	27% helix, 35% strand	Q8ST28
B	Tata-box-binding protein	protein	179	26% helix, 36% strand	Q8ST28

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 6 copies · chains A, B

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

Pockets

5 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	157	0.47	0.77	30	EDO
2	55	0.47	0.85	20	EDO
3	67	0.44	0.82	17	EDO
4	134	0.40	0.74	25	empty
5	53	0.26	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 1583 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3EIK · double stranded DNA binding protein · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8ST28
Elsewhere: RCSB PDB 3EIK · PDBe 3EIK · UniProt Q8ST28

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