scPDB - 1mdu entry

Protein Data Bank Entry:

PDB ID : 1mdu

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-08-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Actin, alpha skeletal muscle
ID:	ACTS_CHICK
AC:	P68139
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.344
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.350	725.625

% Hydrophobic	% Polar
43.26	56.74
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	69.98 %
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
13.8817	29.6995	55.4307

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
O1G	OG	SER- 16	2.84	164.32	H-Bond (Protein Donor)	false
O1G	N	SER- 16	2.99	172.2	H-Bond (Protein Donor)	false
O3B	N	SER- 16	3.44	126.2	H-Bond (Protein Donor)	false
O1B	N	GLY- 17	3.23	149.41	H-Bond (Protein Donor)	false
O1B	N	LEU- 18	2.89	154.32	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 20	3.69	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 20	2.98	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 20	3.32	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 20	3.32	146.19	H-Bond (Protein Donor)	false
O3B	N	ASP- 159	3	173.45	H-Bond (Protein Donor)	false
O3A	N	ASP- 159	3.33	124.92	H-Bond (Protein Donor)	false
C3'	CB	ASP- 159	3.9	0	Hydrophobic	false
O2G	N	GLY- 160	2.72	151.69	H-Bond (Protein Donor)	false
O2G	N	VAL- 161	2.8	162.97	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 215	3	160.19	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 216	2.7	156.31	H-Bond (Ligand Donor)	false
O1A	N	GLY- 304	2.8	172.17	H-Bond (Protein Donor)	false
O3G	CA	CA- 401	2.48	0	Metal Acceptor	false
O2B	CA	CA- 401	2.3	0	Metal Acceptor	false