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Structure-based design of synthetic azobenzene ligands for streptavidin

Analyse Structure-based design of synthetic azobenzene ligands for streptavidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SRH
Type: protein
Length: 232 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: MOB
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Streptavidin	protein	116	3% helix, 59% strand	P22629

Ligands and binding sites

MOB · 2-((3',5'-dimethoxy-4'-hydroxyphenyl)azo)benzoic acid · ligand · 2 copies · chains B, A

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	111	0.47	0.79	20	MOB
2	92	0.46	0.80	19	MOB

Interfaces

1 interface between chains.

A–B · 1614 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1SRH · Structure-based design of synthetic azobenzene ligands for streptavidin · 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 1SRH · PDBe 1SRH · UniProt P22629

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