scPDB - 1sri entry

Protein Data Bank Entry:

PDB ID : 1sri

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 1994-02-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Streptavidin
ID:	SAV_STRAV
AC:	P22629
Organism:	Streptomyces avidinii
Reign:	Bacteria
TaxID:	1895
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	18.396
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.940	303.750

% Hydrophobic	% Polar
66.67	33.33
According to VolSite

Ligand :

HET Code:	DMB
Formula:	C15H13N2O3
Molecular weight:	269.275 g/mol
DrugBank ID:	DB07667
Buried Surface Area:	76.46 %
Polar Surface area:	85.08 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
19.7521	4.6863	13.8985

Binding mode :

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O	ND2	ASN- 23	2.91	134.42	H-Bond (Protein Donor)	false
O	OG	SER- 27	2.8	152.51	H-Bond (Protein Donor)	false
OXT	OG	SER- 27	3.33	143.8	H-Bond (Protein Donor)	false
C3'	CB	ALA- 50	3.94	0	Hydrophobic	false
CM3	CE3	TRP- 79	3.48	0	Hydrophobic	false
C4'	CB	TRP- 79	4.01	0	Hydrophobic	false
C4'	CB	ALA- 86	3.83	0	Hydrophobic	false
CM5	CB	ALA- 86	4.49	0	Hydrophobic	false
CM5	CB	SER- 88	3.67	0	Hydrophobic	false
C5	CG2	THR- 90	3.92	0	Hydrophobic	false
C4	CE2	TRP- 108	3	0	Hydrophobic	false
C6	CD2	LEU- 110	4.06	0	Hydrophobic	false
C1'	CD2	LEU- 110	3.83	0	Hydrophobic	false
CM5	CD1	LEU- 110	3.55	0	Hydrophobic	false
C6'	CD2	LEU- 110	3.62	0	Hydrophobic	false