scPDB - 2zt5 entry

Protein Data Bank Entry:

PDB ID : 2zt5

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycine--tRNA ligase
ID:	SYG_HUMAN
AC:	P41250
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	62.385
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.197	1012.500

% Hydrophobic	% Polar
25.67	74.33
According to VolSite

Ligand :

HET Code:	B4P
Formula:	C20H24N10O19P4
Molecular weight:	832.355 g/mol
DrugBank ID:	-
Buried Surface Area:	56.85 %
Polar Surface area:	484.53 Å2

Number of
H-Bond Acceptors:	27
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
31.3334	-16.0774	75.9348

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
O2A	OD1	ASP- 146	2.93	154.94	H-Bond (Protein Donor)	false
O3A	NH1	ARG- 159	3.11	157.71	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 277	2.83	173.94	H-Bond (Protein Donor)	false
O1D	NH2	ARG- 277	2.67	173.57	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 277	3.73	0	Ionic (Protein Cationic)	false
O1D	CZ	ARG- 277	3.56	0	Ionic (Protein Cationic)	false
O2A	OE2	GLU- 279	2.52	141.88	H-Bond (Protein Donor)	false
N6B	OE1	GLU- 279	3.1	128.59	H-Bond (Ligand Donor)	false
O1B	CZ	ARG- 288	3.54	0	Ionic (Protein Cationic)	false
N6B	O	VAL- 289	2.84	121.66	H-Bond (Ligand Donor)	false
N1B	N	VAL- 289	3.16	166.78	H-Bond (Protein Donor)	false
C1F	CE2	PHE- 292	3.77	0	Hydrophobic	false
DuAr	DuAr	PHE- 292	3.72	0	Aromatic Face/Face	false
C5F	CE	MET- 294	4.46	0	Hydrophobic	false
C1F	CE	MET- 294	4.43	0	Hydrophobic	false
N6A	O	ASN- 381	3.12	121.02	H-Bond (Ligand Donor)	false
C3F	CG	GLU- 403	4.43	0	Hydrophobic	false
O3F	OE2	GLU- 403	2.89	156.38	H-Bond (Ligand Donor)	false
O2F	O	ILE- 404	3.32	153.16	H-Bond (Ligand Donor)	false
C5F	CB	SER- 524	3.76	0	Hydrophobic	false
O1B	NH1	ARG- 529	3.29	135.6	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 529	2.93	153.58	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 529	3.54	0	Ionic (Protein Cationic)	false
C2F	CD	ARG- 529	3.72	0	Hydrophobic	false