scPDB - 1rxh entry

Protein Data Bank Entry:

PDB ID : 1rxh

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2003-12-18

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:	35.747
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.799	320.625

% Hydrophobic	% Polar
61.05	38.95
According to VolSite

Ligand :

HET Code:	BNI
Formula:	C16H20N4O4S
Molecular weight:	364.419 g/mol
DrugBank ID:	DB03549
Buried Surface Area:	64.53 %
Polar Surface area:	141.35 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
35.223	37.9918	6.52432

Binding mode :

What is Poseview ?

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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
O3	ND2	ASN- 223	2.64	144.15	H-Bond (Protein Donor)	false
O3	OG	SER- 227	2.93	137.88	H-Bond (Protein Donor)	false
C7	CB	SER- 245	3.87	0	Hydrophobic	false
N2	OG	SER- 245	3.23	163.12	H-Bond (Ligand Donor)	false
C7	CG2	VAL- 247	3.77	0	Hydrophobic	false
O2	N	ASN- 249	3.35	122.07	H-Bond (Protein Donor)	false
C9	CB	ALA- 250	4.2	0	Hydrophobic	false
C10	CD2	TRP- 279	3.42	0	Hydrophobic	false
C9	CE2	TRP- 279	4.14	0	Hydrophobic	false
S1	CZ2	TRP- 279	3.56	0	Hydrophobic	false
C7	CZ2	TRP- 279	3.99	0	Hydrophobic	false
C20	CB	ALA- 286	4.41	0	Hydrophobic	false
C20	CB	SER- 288	4.08	0	Hydrophobic	false
S1	CG2	THR- 290	3.98	0	Hydrophobic	false
S1	CZ2	TRP- 292	3.82	0	Hydrophobic	false
C6	CE2	TRP- 308	3.5	0	Hydrophobic	false
C8	CD1	LEU- 310	4.09	0	Hydrophobic	false
C24	CD1	LEU- 310	3.89	0	Hydrophobic	false
C21	CB	SER- 312	4.06	0	Hydrophobic	false
C23	CD	ARG- 324	4.17	0	Hydrophobic	false
O27	CZ	ARG- 324	3.03	0	Ionic (Protein Cationic)	false
N1	OD2	ASP- 328	2.69	153.26	H-Bond (Ligand Donor)	false