scPDB - 5ks7 entry

Protein Data Bank Entry:

PDB ID : 5ks7

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2016-07-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carnitine transport ATP-binding protein OpuCA
ID:	OPUCA_LISMN
AC:	Q9KHT9
Organism:	Listeria monocytogenes
Reign:	Bacteria
TaxID:	1639
EC Number:	3.6.3.32

Chains:

Chain Name:	Percentage of Residues within binding site
A	51 %
B	49 %

Ligand binding site composition:

B-Factor:	21.995
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.068	931.500

% Hydrophobic	% Polar
42.03	57.97
According to VolSite

Ligand :

HET Code:	2BA
Formula:	C20H22N10O12P2
Molecular weight:	656.396 g/mol
DrugBank ID:	-
Buried Surface Area:	72.66 %
Polar Surface area:	334.95 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	4
Rings:	7
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-22.5291	3.61686	-18.2995

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
N6	O	VAL- 260	2.9	130.6	H-Bond (Ligand Donor)	false
N61	O	VAL- 260	3.1	145.72	H-Bond (Ligand Donor)	false
N1	N	VAL- 260	2.86	171.35	H-Bond (Protein Donor)	false
N11	N	VAL- 260	3.07	150.45	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 280	3.93	0	Hydrophobic	false
C1'1	CG1	VAL- 280	4	0	Hydrophobic	false
N7	OG1	THR- 282	2.74	144.94	H-Bond (Protein Donor)	false
N71	OG1	THR- 282	2.65	148.21	H-Bond (Protein Donor)	false
N6	O	THR- 282	3.41	131.21	H-Bond (Ligand Donor)	false
N61	OG1	THR- 282	3.46	152.13	H-Bond (Ligand Donor)	false
N61	O	THR- 282	3.47	121.16	H-Bond (Ligand Donor)	false
C2'	CD2	TYR- 342	4.16	0	Hydrophobic	false
C2'1	CD2	TYR- 342	4.15	0	Hydrophobic	false
C1'1	CG2	THR- 357	4.1	0	Hydrophobic	false
O1P	N	ARG- 358	3.2	150.95	H-Bond (Protein Donor)	false
O1P1	N	ARG- 358	3.34	167.87	H-Bond (Protein Donor)	false
O2P	N	ALA- 359	3.12	166.14	H-Bond (Protein Donor)	false
O2P1	N	ALA- 359	2.99	147.37	H-Bond (Protein Donor)	false