scPDB - 3syt entry

Protein Data Bank Entry:

PDB ID : 3syt

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2011-07-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamine-dependent NAD(+) synthetase
ID:	NADE_MYCTU
AC:	P9WJJ3
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	6.3.5.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	36 %
D	64 %

Ligand binding site composition:

B-Factor:	42.941
Number of residues:	47
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	AMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.740	931.500

% Hydrophobic	% Polar
39.13	60.87
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	58.53 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
1.42445	63.9434	-37.1756

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
N1A	NH1	ARG- 354	3.01	137.7	H-Bond (Protein Donor)	false
C3D	CG2	VAL- 452	4.33	0	Hydrophobic	false
O3	ND2	ASN- 456	3.29	151.01	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 471	2.79	178.93	H-Bond (Protein Donor)	false
O3B	O	GLY- 475	3.21	175.42	H-Bond (Ligand Donor)	false
C1B	CG2	ILE- 476	4.06	0	Hydrophobic	false
N7N	OE2	GLU- 485	3.21	160.32	H-Bond (Ligand Donor)	false
C2D	CZ2	TRP- 490	4.34	0	Hydrophobic	false
C5N	CB	THR- 492	4.27	0	Hydrophobic	false
O1A	N	TYR- 493	2.74	159.59	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 497	3.26	137.7	H-Bond (Ligand Donor)	false
C5B	CZ	PHE- 634	4.34	0	Hydrophobic	false
C1B	CZ	PHE- 634	4.19	0	Hydrophobic	false
DuAr	DuAr	PHE- 634	3.65	0	Aromatic Face/Face	false
O1A	NZ	LYS- 635	3.08	0	Ionic (Protein Cationic)	false
N6A	O	SER- 661	3.17	138.18	H-Bond (Ligand Donor)	false
O2A	O	HOH- 704	2.56	179.95	H-Bond (Protein Donor)	false