scPDB - 5bn3 entry

Protein Data Bank Entry:

PDB ID : 5bn3

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2015-05-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	V-type ATP synthase alpha chain	NEQ263
ID:	VATA_NANEQ	Q74MS5_NANEQ
AC:	Q74MJ7	Q74MS5
Organism:	Nanoarchaeum equitans
Reign:	Archaea
TaxID:	228908
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	75 %
B	25 %

Ligand binding site composition:

B-Factor:	37.418
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.216	1174.500

% Hydrophobic	% Polar
50.57	49.43
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	68.52 %
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
-19.8439	22.3349	-23.9575

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
O3B	N	GLY- 226	2.8	160.2	H-Bond (Protein Donor)	false
O1B	N	GLY- 228	2.87	151.62	H-Bond (Protein Donor)	false
O3A	N	GLY- 228	3.04	121.23	H-Bond (Protein Donor)	false
O1B	N	LYS- 229	2.89	152.81	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 229	2.56	130.09	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 229	2.56	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 229	3.9	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 229	3.71	0	Ionic (Protein Cationic)	false
O2B	N	THR- 230	3.1	157.98	H-Bond (Protein Donor)	false
O1A	N	VAL- 231	2.84	165.27	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 231	3.82	0	Hydrophobic	false
C5'	CD2	LEU- 324	4.47	0	Hydrophobic	false
C4'	CD1	LEU- 324	4.36	0	Hydrophobic	false
O3B	NH1	ARG- 326	2.68	141.88	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 326	3.35	122.09	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 326	2.72	128.54	H-Bond (Protein Donor)	false
O3A	NH1	ARG- 326	3.18	127.92	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 326	3.4	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 326	3.93	0	Ionic (Protein Cationic)	false
C3'	CG	ARG- 326	4.49	0	Hydrophobic	false
O3'	O	ARG- 326	3.38	155.81	H-Bond (Ligand Donor)	false
C1'	CZ	TYR- 414	3.79	0	Hydrophobic	false
N6	O	GLN- 491	2.97	144.41	H-Bond (Ligand Donor)	false
N1	N	ALA- 493	2.96	172	H-Bond (Protein Donor)	false
C2'	CE2	PHE- 494	4.21	0	Hydrophobic	false
O2B	MG	MG- 609	2.07	0	Metal Acceptor	false