scPDB - 1nj5 entry

Protein Data Bank Entry:

PDB ID : 1nj5

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2002-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proline--tRNA ligase
ID:	SYP_METTH
AC:	O26708
Organism:	Methanothermobacter thermautotrophicus
Reign:	Archaea
TaxID:	187420
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	56.044
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.110	664.875

% Hydrophobic	% Polar
31.98	68.02
According to VolSite

Ligand :

HET Code:	P5A
Formula:	C15H21N7O7S
Molecular weight:	443.435 g/mol
DrugBank ID:	DB02510
Buried Surface Area:	78.25 %
Polar Surface area:	218.83 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-31.8594	-81.7065	-36.187

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
N	OG1	THR- 117	2.81	141.21	H-Bond (Ligand Donor)	false
N	OE1	GLU- 119	3.79	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 119	2.65	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 119	2.65	141.28	H-Bond (Ligand Donor)	false
O	NH2	ARG- 148	3.03	133.56	H-Bond (Protein Donor)	false
O1S	NH1	ARG- 148	3.07	143.54	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 148	3.14	140.33	H-Bond (Protein Donor)	false
N6	OE1	GLU- 150	3.14	137.28	H-Bond (Ligand Donor)	false
N1	N	VAL- 160	3.36	163.01	H-Bond (Protein Donor)	false
N6	O	VAL- 160	3.23	137.4	H-Bond (Ligand Donor)	false
CG	CZ	PHE- 166	4.03	0	Hydrophobic	false
C5'	CE1	PHE- 166	3.81	0	Hydrophobic	false
CG	CB	GLU- 168	3.57	0	Hydrophobic	false
O2'	O	GLN- 232	2.8	157.85	H-Bond (Ligand Donor)	false
O3'	OE1	GLN- 232	3.2	145.56	H-Bond (Ligand Donor)	false
O2S	OG1	THR- 235	3	165.04	H-Bond (Protein Donor)	false
C3'	CG2	THR- 235	4.29	0	Hydrophobic	false
N3S	NE2	HIS- 237	3.19	155.36	H-Bond (Ligand Donor)	false
CB	SG	CYS- 265	3.89	0	Hydrophobic	false
C1'	CB	SER- 269	3.65	0	Hydrophobic	false
N3	OG	SER- 269	2.69	170.68	H-Bond (Protein Donor)	false
C2'	CD	ARG- 271	4.12	0	Hydrophobic	false