scPDB - 3ck7 entry

Protein Data Bank Entry:

PDB ID : 3ck7

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-03-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Starch-binding protein SusD
ID:	SUSD_BACTN
AC:	Q8A1G2
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	50 %
D	50 %

Ligand binding site composition:

B-Factor:	13.407
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.620	627.750

% Hydrophobic	% Polar
37.63	62.37
According to VolSite

Ligand :

HET Code:	ACX
Formula:	C36H60O30
Molecular weight:	972.844 g/mol
DrugBank ID:	DB01909
Buried Surface Area:	58.89 %
Polar Surface area:	474.9 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	18
Rings:	8
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
7.20521	-19.7786	102.648

Binding mode :

What is Poseview ?

2D View
3D View

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
O2B	NH1	ARG- 81	2.71	172.16	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 81	3	157.57	H-Bond (Protein Donor)	false
O2E	NH1	ARG- 81	2.71	165.78	H-Bond (Protein Donor)	false
O3E	NH2	ARG- 81	2.95	159.15	H-Bond (Protein Donor)	false
C2A	CZ2	TRP- 96	3.93	0	Hydrophobic	false
C2D	CZ2	TRP- 96	4.05	0	Hydrophobic	false
C4A	CE2	TRP- 98	4.08	0	Hydrophobic	false
C6A	CZ2	TRP- 98	4.39	0	Hydrophobic	false
C4D	CD2	TRP- 98	3.82	0	Hydrophobic	false
C3A	CB	TRP- 98	4.28	0	Hydrophobic	false
C1C	CZ3	TRP- 98	3.44	0	Hydrophobic	false
C3D	CB	TRP- 98	4.48	0	Hydrophobic	false
C6D	CE2	TRP- 98	3.79	0	Hydrophobic	false
C1F	CZ3	TRP- 98	3.62	0	Hydrophobic	false
O2A	OD1	ASN- 101	2.64	175.5	H-Bond (Ligand Donor)	false
O2D	OD1	ASN- 101	2.58	169.01	H-Bond (Ligand Donor)	false
O3A	ND2	ASN- 101	2.94	155.4	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 101	2.83	164.45	H-Bond (Protein Donor)	false
C1B	CG	TYR- 296	4.23	0	Hydrophobic	false
C5C	CZ	TYR- 296	4.31	0	Hydrophobic	false
C6C	CE2	TYR- 296	3.78	0	Hydrophobic	false
C1E	CD2	TYR- 296	4.18	0	Hydrophobic	false
C4F	CE1	TYR- 296	3.84	0	Hydrophobic	false
C5F	CZ	TYR- 296	4.13	0	Hydrophobic	false
C6F	CE2	TYR- 296	3.44	0	Hydrophobic	false
C4C	CE1	TYR- 296	3.86	0	Hydrophobic	false
C3F	CE1	TYR- 296	4.21	0	Hydrophobic	false
O6C	ND2	ASN- 318	3.38	120.4	H-Bond (Protein Donor)	false
O6A	O	TRP- 320	2.51	124.87	H-Bond (Ligand Donor)	false
O6D	O	TRP- 320	2.75	141.98	H-Bond (Ligand Donor)	false
C1B	CH2	TRP- 320	3.66	0	Hydrophobic	false
C4B	CE3	TRP- 320	4.04	0	Hydrophobic	false
C6C	CZ2	TRP- 320	4.43	0	Hydrophobic	false
C1E	CH2	TRP- 320	3.8	0	Hydrophobic	false
C2E	CZ3	TRP- 320	3.85	0	Hydrophobic	false
C4E	CE3	TRP- 320	4.19	0	Hydrophobic	false
C6F	CZ2	TRP- 320	4.39	0	Hydrophobic	false
C2B	CZ3	TRP- 320	3.52	0	Hydrophobic	false
C6B	CD2	TRP- 320	3.87	0	Hydrophobic	false
C6E	CD2	TRP- 320	3.67	0	Hydrophobic	false
C5D	SG	CYS- 322	4.44	0	Hydrophobic	false
C1A	SG	CYS- 322	3.43	0	Hydrophobic	false
C1D	SG	CYS- 322	3.35	0	Hydrophobic	false
O3F	O	HOH- 906	3.03	164.76	H-Bond (Protein Donor)	false