scPDB - 2d3a entry

Protein Data Bank Entry:

PDB ID : 2d3a

Resolution :2.630 Å

Experimental Method : X-ray

Deposition Date : 2005-09-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamine synthetase root isozyme 3
ID:	GLNA3_MAIZE
AC:	P38561
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	6.3.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
I	17 %
J	83 %

Ligand binding site composition:

B-Factor:	62.830
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	4
Water Molecules:	1
Cofactors:
Metals:	MN MN MN

Cavity properties

Ligandability	Volume (Å3)
0.749	1144.125

% Hydrophobic	% Polar
36.58	63.42
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	62.45 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
68.0957	27.4847	-5.20541

Binding mode :

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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
O3'	OG	SER- 187	2.52	167.72	H-Bond (Ligand Donor)	false
C3'	CB	SER- 187	4.19	0	Hydrophobic	false
C3'	CB	GLN- 201	4.16	0	Hydrophobic	false
C1'	CG	PRO- 204	4.44	0	Hydrophobic	false
C4'	CB	ASN- 251	4.22	0	Hydrophobic	false
N6	OG	SER- 253	3.01	142.66	H-Bond (Ligand Donor)	false
N1	OG	SER- 253	2.99	155.47	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 316	2.83	168.83	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 316	3.44	178.45	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 316	3.79	0	Ionic (Protein Cationic)	false
O3B	MN	MN- 1091	1.99	0	Metal Acceptor	false
O2A	MN	MN- 1091	2.21	0	Metal Acceptor	false
O1B	MN	MN- 1092	2.08	0	Metal Acceptor	false