scPDB - 3afh entry

Protein Data Bank Entry:

PDB ID : 3afh

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-03-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate--tRNA ligase 2
ID:	SYE2_THEMA
AC:	Q9X2I8
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:	21.113
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.515	563.625

% Hydrophobic	% Polar
35.93	64.07
According to VolSite

Ligand :

HET Code:	GSU
Formula:	C15H20N7O9S
Molecular weight:	474.426 g/mol
DrugBank ID:	-
Buried Surface Area:	63.03 %
Polar Surface area:	269.99 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
18.2642	62.8976	3.28934

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
OE1	CZ	ARG- 28	3.56	0	Ionic (Protein Cationic)	false
OE2	CZ	ARG- 28	3.85	0	Ionic (Protein Cationic)	false
OE1	NH1	ARG- 28	2.88	155.25	H-Bond (Protein Donor)	false
OE1	NH2	ARG- 28	3.37	132.61	H-Bond (Protein Donor)	false
OE2	NH2	ARG- 28	2.92	166.39	H-Bond (Protein Donor)	false
C4'	CE1	PHE- 29	3.8	0	Hydrophobic	false
N	O	ALA- 30	2.78	167.65	H-Bond (Ligand Donor)	false
CB	CB	ALA- 30	4.43	0	Hydrophobic	false
N	OG	SER- 32	2.91	148.78	H-Bond (Ligand Donor)	false
O2S	N	SER- 32	3.13	161.9	H-Bond (Protein Donor)	false
C4'	CG2	THR- 44	4.49	0	Hydrophobic	false
N	OE1	GLU- 64	2.75	130.51	H-Bond (Ligand Donor)	false
N	OE1	GLU- 64	2.75	0	Ionic (Ligand Cationic)	false
CG	CG2	VAL- 202	4.47	0	Hydrophobic	false
OE2	NH1	ARG- 216	2.94	147.78	H-Bond (Protein Donor)	false
OE2	CZ	ARG- 216	3.89	0	Ionic (Protein Cationic)	false
O3'	N	GLY- 217	3.22	172.39	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 219	2.56	144.06	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 219	3.5	146.73	H-Bond (Ligand Donor)	false
O	NE2	HIS- 220	2.8	155.05	H-Bond (Protein Donor)	false
N1	N	ILE- 247	2.84	171.88	H-Bond (Protein Donor)	false
N6	O	ILE- 247	3.32	169.24	H-Bond (Ligand Donor)	false
OE2	O	HOH- 1005	2.74	179.96	H-Bond (Protein Donor)	false