scPDB - 1xef entry

Protein Data Bank Entry:

PDB ID : 1xef

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2004-09-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-hemolysin translocation ATP-binding protein HlyB
ID:	HLYBP_ECOLX
AC:	P08716
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	61 %
D	39 %

Ligand binding site composition:

B-Factor:	46.962
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.466	2068.875

% Hydrophobic	% Polar
39.64	60.36
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	63.31 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.5159	38.5647	9.52671

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
C1'	CE2	TYR- 477	4.25	0	Hydrophobic	false
DuAr	DuAr	TYR- 477	3.58	0	Aromatic Face/Face	false
C5'	CG2	ILE- 484	3.82	0	Hydrophobic	false
C4'	CD1	ILE- 484	3.84	0	Hydrophobic	false
C1'	CD1	ILE- 484	4.19	0	Hydrophobic	false
O1G	OG	SER- 504	2.71	175.7	H-Bond (Protein Donor)	false
O3B	N	GLY- 505	2.71	151.69	H-Bond (Protein Donor)	false
O1B	N	SER- 506	3.28	128.61	H-Bond (Protein Donor)	false
O1B	N	GLY- 507	3.18	145.86	H-Bond (Protein Donor)	false
O3A	N	GLY- 507	3.43	142.3	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 508	2.76	150.33	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 508	2.83	163.16	H-Bond (Protein Donor)	false
O1B	N	LYS- 508	2.96	149.36	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 508	2.76	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 508	2.83	0	Ionic (Protein Cationic)	false
O2B	N	SER- 509	3.12	158.19	H-Bond (Protein Donor)	false
O2A	OG1	THR- 510	2.71	159.86	H-Bond (Protein Donor)	false
O2A	N	THR- 510	3.01	161.38	H-Bond (Protein Donor)	false
O1G	OG	SER- 607	2.77	163.52	H-Bond (Protein Donor)	false
O3B	OG	SER- 607	3.39	124.98	H-Bond (Protein Donor)	false
C2'	CB	SER- 607	4.43	0	Hydrophobic	false
O1G	N	GLY- 609	2.71	141.42	H-Bond (Protein Donor)	false
O2'	OE1	GLN- 610	2.82	154.21	H-Bond (Ligand Donor)	false
O3G	MG	MG- 2801	1.89	0	Metal Acceptor	false
O2B	MG	MG- 2801	2.1	0	Metal Acceptor	false