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Wild-type streptavidin in complex with love-hate ligand 3 (LH3)

Analyse Wild-type streptavidin in complex with love-hate ligand 3 (LH3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CPF
Type: protein
Length: 239 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: LH3
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Streptavidin	protein	119	5% helix, 57% strand	P22629
B	Streptavidin	protein	120	8% helix, 56% strand	P22629

Ligands and binding sites

LH3 · methyl 4-(2-{5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H- thieno[3,4-d]imidazolidin-4-yl]pentanehydrazido}-3- [4-(methoxycarbonyl)phenyl]phenyl)benzoate · ligand · chains B

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

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	89	0.46	0.81	22	empty
2	60	0.32	0.76	18	empty
3	69	0.32	0.74	18	LH3

Interfaces

1 interface between chains.

A–B · 1574 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

4CPF · Wild-type streptavidin in complex with love-hate ligand 3 (LH3) · 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 4CPF · PDBe 4CPF · UniProt P22629

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