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Crystal structure of a triple-mutant of streptavidin in complex with desthiobiotin

Analyse Crystal structure of a triple-mutant of streptavidin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DNE
Type: protein
Length: 241 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: DTB, SO4
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Streptavidin	protein	121	5% helix, 57% strand	P22629
B	Streptavidin	protein	120	5% helix, 57% strand	P22629

Ligands and binding sites

DTB · 6-(5-methyl-2-oxo-imidazolidin-4-yl)-hexanoic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B

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

Pockets

2 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	95	0.49	0.81	17	DTB
2	91	0.42	0.78	18	DTB

Interfaces

1 interface between chains.

A–B · 1631 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

4DNE · Crystal structure of a triple-mutant of streptavidin in complex with desthiobiotin · 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 P22629
Elsewhere: RCSB PDB 4DNE · PDBe 4DNE · UniProt P22629

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