scPDB - 4wbd entry

Protein Data Bank Entry:

PDB ID : 4wbd

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2014-09-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative cysteine ligase BshC
ID:	BSHC_BACSU
AC:	P55342
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.736
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.586	479.250

% Hydrophobic	% Polar
49.30	50.70
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	52.42 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
29.3357	-4.63663	15.0071

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
O1A	OG	SER- 146	2.89	169.66	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 384	2.64	155.54	H-Bond (Ligand Donor)	false
O3'	NE2	HIS- 386	2.91	154.64	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 386	3.17	129.17	H-Bond (Protein Donor)	false
C4'	CD1	ILE- 387	4.48	0	Hydrophobic	false
O2B	NE	ARG- 490	3.28	136.16	H-Bond (Protein Donor)	false
O3B	NE	ARG- 490	3.44	163.69	H-Bond (Protein Donor)	false
C5'	CG	ARG- 490	3.9	0	Hydrophobic	false
C4'	CB	ARG- 490	4.47	0	Hydrophobic	false
O5'	ND2	ASN- 493	3.31	129.91	H-Bond (Protein Donor)	false
O4'	ND2	ASN- 493	3.13	151.34	H-Bond (Protein Donor)	false
C5'	CB	ASN- 493	4.05	0	Hydrophobic	false
C4'	CB	SER- 494	4.42	0	Hydrophobic	false
C1'	CB	SER- 494	3.93	0	Hydrophobic	false
DuAr	DuAr	TRP- 506	3.81	0	Aromatic Face/Face	false
DuAr	DuAr	TYR- 510	3.7	0	Aromatic Face/Face	false
C2'	CZ	TYR- 510	3.94	0	Hydrophobic	false