scPDB - 4yer entry

Protein Data Bank Entry:

PDB ID : 4yer

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2015-02-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Antibiotic ABC transporter, ATP-binding protein, putative
ID:	Q9X1C3_THEMA
AC:	Q9X1C3
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	36 %
B	64 %

Ligand binding site composition:

B-Factor:	57.296
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.618	1859.625

% Hydrophobic	% Polar
36.66	63.34
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	56 %
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
0.590815	-39.0081	75.9473

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
DuAr	DuAr	PHE- 14	3.85	0	Aromatic Face/Face	false
C1'	CE2	PHE- 17	3.58	0	Hydrophobic	false
C4'	CB	ALA- 19	4.29	0	Hydrophobic	false
O2B	N	GLY- 40	2.71	164.18	H-Bond (Protein Donor)	false
O3'	O	GLY- 40	3.42	136.39	H-Bond (Ligand Donor)	false
O3B	N	ALA- 41	3.32	123.65	H-Bond (Protein Donor)	false
O3B	N	GLY- 42	3.42	128.24	H-Bond (Protein Donor)	false
O3A	N	GLY- 42	3.04	148.21	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 43	3.91	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 43	2.58	0	Ionic (Protein Cationic)	false
O3B	N	LYS- 43	3.12	159.25	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 43	2.58	156.42	H-Bond (Protein Donor)	false
O1B	N	THR- 44	3.07	157.73	H-Bond (Protein Donor)	false
O2A	OG1	THR- 45	2.67	161.44	H-Bond (Protein Donor)	false
O2A	N	THR- 45	3	157.09	H-Bond (Protein Donor)	false
N6	O	LYS- 134	3.48	146.74	H-Bond (Ligand Donor)	false
C2'	CB	SER- 137	3.55	0	Hydrophobic	false