scPDB - 4yvn entry

Protein Data Bank Entry:

PDB ID : 4yvn

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Spore coat protein A
ID:	COTA_BACSU
AC:	P07788
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:	34.065
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.472	263.250

% Hydrophobic	% Polar
62.82	37.18
According to VolSite

Ligand :

HET Code:	EBS
Formula:	C18H16N4O6S4
Molecular weight:	512.603 g/mol
DrugBank ID:	-
Buried Surface Area:	42.35 %
Polar Surface area:	212.96 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	0
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
22.0662	-51.2353	-28.4117

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
C3	CB	PRO- 359	4	0	Hydrophobic	false
O45	N	SER- 360	3.05	142.39	H-Bond (Protein Donor)	false
C3	CB	SER- 360	4.29	0	Hydrophobic	false
S18	CB	HIS- 363	4.41	0	Hydrophobic	false
C24	CB	HIS- 363	4.08	0	Hydrophobic	false
S9	CB	HIS- 363	3.99	0	Hydrophobic	false
S18	CD1	ILE- 366	4.12	0	Hydrophobic	false
C24	CG2	THR- 406	3.37	0	Hydrophobic	false
C12	CD1	ILE- 408	4	0	Hydrophobic	false
S9	CG	ARG- 429	4.2	0	Hydrophobic	false
C10	CD2	LEU- 431	3.57	0	Hydrophobic	false
C12	CD1	LEU- 431	3.66	0	Hydrophobic	false
C22	CD2	LEU- 431	3.87	0	Hydrophobic	false
C11	CD2	LEU- 431	3.5	0	Hydrophobic	false
O39	NH2	ARG- 476	3.1	162.35	H-Bond (Protein Donor)	false
O49	NH1	ARG- 476	3.06	171.77	H-Bond (Protein Donor)	false
O39	CZ	ARG- 476	3.85	0	Ionic (Protein Cationic)	false
O49	CZ	ARG- 476	3.9	0	Ionic (Protein Cationic)	false
S18	CB	ALA- 478	3.8	0	Hydrophobic	false
C25	CB	ALA- 478	3.91	0	Hydrophobic	false
C4	CB	THR- 480	4.4	0	Hydrophobic	false