scPDB - 2cv2 entry

Protein Data Bank Entry:

PDB ID : 2cv2

Resolution :2.690 Å

Experimental Method : X-ray

Deposition Date : 2005-05-31

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
ID:	SYE_THET8
AC:	P27000
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	6.1.1.17

Chains:

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

Ligand binding site composition:

B-Factor:	22.914
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.531	880.875

% Hydrophobic	% Polar
38.70	61.30
According to VolSite

Ligand :

HET Code:	GSU
Formula:	C15H20N7O9S
Molecular weight:	474.426 g/mol
DrugBank ID:	-
Buried Surface Area:	72.44 %
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
36.1173	78.6485	53.5778

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
OE1	NH1	ARG- 5	3.17	131.94	H-Bond (Protein Donor)	false
OE1	NH2	ARG- 5	3.15	132.53	H-Bond (Protein Donor)	false
OE1	CZ	ARG- 5	3.55	0	Ionic (Protein Cationic)	false
OE2	CZ	ARG- 5	3.71	0	Ionic (Protein Cationic)	false
C4'	CD1	ILE- 6	4.2	0	Hydrophobic	false
N	O	ALA- 7	2.58	154.98	H-Bond (Ligand Donor)	false
N10	O	ALA- 7	3.5	123.53	H-Bond (Ligand Donor)	false
CB	CB	ALA- 7	3.91	0	Hydrophobic	false
O2S	N	SER- 9	2.94	154.24	H-Bond (Protein Donor)	false
C4'	CB	ILE- 21	4.39	0	Hydrophobic	false
C1'	CG1	ILE- 21	3.6	0	Hydrophobic	false
N	OE1	GLU- 41	2.73	175.77	H-Bond (Ligand Donor)	false
N	OE1	GLU- 41	2.73	0	Ionic (Ligand Cationic)	false
OE1	OH	TYR- 187	2.68	157.79	H-Bond (Protein Donor)	false
CG	CE1	TYR- 187	3.39	0	Hydrophobic	false
OE1	ND2	ASN- 191	3.29	141.01	H-Bond (Protein Donor)	false
OE1	NH2	ARG- 205	3.25	147.52	H-Bond (Protein Donor)	false
OE1	NE	ARG- 205	3.17	154.58	H-Bond (Protein Donor)	false
OE1	CZ	ARG- 205	3.67	0	Ionic (Protein Cationic)	false
O2'	N	ALA- 206	3.08	152.95	H-Bond (Protein Donor)	false
C1'	CB	ALA- 206	4.34	0	Hydrophobic	false
O2'	OE2	GLU- 208	2.88	156.54	H-Bond (Ligand Donor)	false
CB	CZ2	TRP- 209	4.43	0	Hydrophobic	false
CG	CE2	TRP- 209	3.7	0	Hydrophobic	false
O	NE1	TRP- 209	3.37	129.83	H-Bond (Protein Donor)	false
O2'	NE1	TRP- 209	3.2	125.27	H-Bond (Protein Donor)	false
N1	N	LEU- 236	2.84	167.06	H-Bond (Protein Donor)	false
O1S	O	HOH- 1195	2.78	159.2	H-Bond (Protein Donor)	false