scPDB - 1ses entry

Protein Data Bank Entry:

PDB ID : 1ses

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1994-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine--tRNA ligase
ID:	SYS_THET2
AC:	P34945
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	262724
EC Number:	6.1.1.11

Chains:

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

Ligand binding site composition:

B-Factor:	14.780
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.300	911.250

% Hydrophobic	% Polar
44.07	55.93
According to VolSite

Ligand :

HET Code:	AHX
Formula:	C13H20N7O9P
Molecular weight:	449.313 g/mol
DrugBank ID:	-
Buried Surface Area:	72.54 %
Polar Surface area:	264.67 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
54.4648	12.5294	56.8683

Binding mode :

What is Poseview ?

2D View
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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
O9	OG1	THR- 225	3.01	149.16	H-Bond (Protein Donor)	false
N10	OE1	GLU- 227	3.09	170.06	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 256	3.86	0	Ionic (Protein Cationic)	false
O3A	NH2	ARG- 256	3.17	155.83	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 256	3.24	137.32	H-Bond (Protein Donor)	false
N6	O	VAL- 272	2.78	133.3	H-Bond (Ligand Donor)	false
N1	N	VAL- 272	3.08	172.45	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 275	3.71	0	Hydrophobic	false
DuAr	DuAr	PHE- 275	3.74	0	Aromatic Face/Face	false
C4'	CD	LYS- 277	4.08	0	Hydrophobic	false
N10	OE1	GLU- 279	3.01	138	H-Bond (Ligand Donor)	false
N10	OE2	GLU- 279	2.67	148.77	H-Bond (Ligand Donor)	false
OG	OE1	GLU- 279	2.59	169.24	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 345	2.73	161.97	H-Bond (Ligand Donor)	false
O2'	O	THR- 346	2.81	143.46	H-Bond (Ligand Donor)	false
CB	CB	THR- 380	4.21	0	Hydrophobic	false
C4'	CG2	THR- 380	4.06	0	Hydrophobic	false
OG	OG1	THR- 380	2.77	169.22	H-Bond (Protein Donor)	false
C4'	CB	ALA- 383	4.41	0	Hydrophobic	false
C1'	CB	ALA- 383	3.68	0	Hydrophobic	false
C2'	CD	ARG- 386	4.17	0	Hydrophobic	false