scPDB - 4ys0 entry

Protein Data Bank Entry:

PDB ID : 4ys0

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-03-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein translocase subunit SecA
ID:	SECA_THEMA
AC:	Q9X1R4
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.479
Number of residues:	39
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.844	705.375

% Hydrophobic	% Polar
55.02	44.98
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	65.29 %
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
-22.6337	-8.25819	3.01293

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
N6	O	ARG- 75	2.88	164.04	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 80	2.99	137.25	H-Bond (Protein Donor)	false
N6	OE1	GLN- 80	2.95	143.84	H-Bond (Ligand Donor)	false
O2B	N	GLY- 98	2.78	167.31	H-Bond (Protein Donor)	false
O3B	N	GLY- 100	3	122.88	H-Bond (Protein Donor)	false
O3A	N	GLY- 100	3.12	134.7	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 101	3.96	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 101	3.65	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 101	2.75	0	Ionic (Protein Cationic)	false
O3B	N	LYS- 101	2.88	175.57	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 101	2.75	166.86	H-Bond (Protein Donor)	false
O1A	OG1	THR- 102	2.7	162.53	H-Bond (Protein Donor)	false
O1A	N	THR- 102	3.32	145.62	H-Bond (Protein Donor)	false
C3'	CH2	TRP- 135	4	0	Hydrophobic	false
C2'	CZ2	TRP- 135	3.54	0	Hydrophobic	false
O3'	OD2	ASP- 537	2.98	155.57	H-Bond (Ligand Donor)	false
C3'	CB	ASP- 537	4.15	0	Hydrophobic	false
O1B	MG	MG- 902	2.08	0	Metal Acceptor	false
N1	O	HOH- 1050	2.58	179.97	H-Bond (Protein Donor)	false
O2A	O	HOH- 1099	2.65	161.85	H-Bond (Protein Donor)	false