scPDB - 4u7w entry

Protein Data Bank Entry:

PDB ID : 4u7w

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2014-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	MxaA
ID:	Q93TX2_STIAU
AC:	Q93TX2
Organism:	Stigmatella aurantiaca
Reign:	Bacteria
TaxID:	41
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	19.651
Number of residues:	53
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.647	725.625

% Hydrophobic	% Polar
38.60	61.40
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	62.41 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-4.91604	-27.3943	-5.56208

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
O3B	OG1	THR- 1157	2.55	150.86	H-Bond (Ligand Donor)	false
O2A	N	PHE- 1159	2.89	163.43	H-Bond (Protein Donor)	false
O1N	N	LEU- 1160	3	157.88	H-Bond (Protein Donor)	false
C5D	CB	LEU- 1160	4.26	0	Hydrophobic	false
C4D	CD2	LEU- 1160	4.37	0	Hydrophobic	false
O2X	NH2	ARG- 1181	3.26	142.6	H-Bond (Protein Donor)	false
O2X	NE	ARG- 1181	3.07	155.74	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 1181	2.74	135.46	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 1181	3.6	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 1181	3.79	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 1191	2.52	147.25	H-Bond (Protein Donor)	false
O2X	NH1	ARG- 1191	2.85	171.46	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 1191	3.39	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 1191	3.61	0	Ionic (Protein Cationic)	false
N6A	OD1	ASP- 1216	2.83	168.77	H-Bond (Ligand Donor)	false
N1A	N	ILE- 1217	3.05	161.52	H-Bond (Protein Donor)	false
O4B	N	ALA- 1244	3.35	152.22	H-Bond (Protein Donor)	false
C3D	CB	ALA- 1244	3.94	0	Hydrophobic	false
C2D	CG2	VAL- 1246	3.88	0	Hydrophobic	false
C4D	CG1	VAL- 1281	4.06	0	Hydrophobic	false
C5N	CB	THR- 1283	3.53	0	Hydrophobic	false
O2D	OH	TYR- 1311	2.65	154.89	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 1315	3.1	141.19	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 1315	3.15	142.82	H-Bond (Protein Donor)	false
C5N	CB	PRO- 1337	3.8	0	Hydrophobic	false
O7N	N	VAL- 1340	3.07	161.78	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 1340	4.09	0	Hydrophobic	false
O5B	O	HOH- 1765	3.28	158.51	H-Bond (Protein Donor)	false
O3B	O	HOH- 1773	3.27	122.81	H-Bond (Protein Donor)	false
N3A	O	HOH- 1780	3.07	179.94	H-Bond (Protein Donor)	false
O1A	O	HOH- 1798	2.96	179.95	H-Bond (Protein Donor)	false