scPDB - 1nbm entry

Protein Data Bank Entry:

PDB ID : 1nbm

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 1998-04-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP synthase subunit alpha, mitochondrial
ID:	ATPA_BOVIN
AC:	P19483
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	78 %
D	22 %

Ligand binding site composition:

B-Factor:	50.860
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.566	1032.750

% Hydrophobic	% Polar
33.66	66.34
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	54.15 %
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
97.1876	64.7506	46.5266

Binding mode :

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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
O1B	N	THR- 173	2.94	145.27	H-Bond (Protein Donor)	false
O1B	N	GLY- 174	3.18	173.44	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 175	3.05	135.39	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 175	3.05	0	Ionic (Protein Cationic)	false
O2B	N	THR- 176	2.83	164.81	H-Bond (Protein Donor)	false
O1A	N	SER- 177	2.73	135.24	H-Bond (Protein Donor)	false
O1A	OG	SER- 177	2.62	176.78	H-Bond (Protein Donor)	false
C4'	CZ	PHE- 357	4.19	0	Hydrophobic	false
C2'	CZ	PHE- 357	4.24	0	Hydrophobic	false
C1'	CE2	PHE- 357	3.39	0	Hydrophobic	false
N6	O	GLN- 430	3.26	160.54	H-Bond (Ligand Donor)	false
O2G	MG	MG- 601	1.86	0	Metal Acceptor	false