scPDB - 3zkb entry

Protein Data Bank Entry:

PDB ID : 3zkb

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2013-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA gyrase subunit B
ID:	GYRB_MYCTU
AC:	P9WG45
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
O	92 %
P	8 %

Ligand binding site composition:

B-Factor:	96.616
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.422	327.375

% Hydrophobic	% Polar
47.42	52.58
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	85.04 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-90.3469	43.834	40.2628

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
C4'	CD1	ILE- 17	4.38	0	Hydrophobic	false
C2'	CD1	ILE- 17	4.48	0	Hydrophobic	false
O2A	ND2	ASN- 52	3.13	142.21	H-Bond (Protein Donor)	false
N6	OD2	ASP- 79	2.82	162.56	H-Bond (Ligand Donor)	false
C1'	CG1	VAL- 99	4.23	0	Hydrophobic	false
C4'	CG2	VAL- 99	3.57	0	Hydrophobic	false
O3'	N	GLY- 107	3.38	141.78	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 108	2.88	160.61	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 108	2.88	0	Ionic (Protein Cationic)	false
C3'	CD	LYS- 108	4.21	0	Hydrophobic	false
C2'	CE1	TYR- 114	4.03	0	Hydrophobic	false
O1G	N	LEU- 120	2.75	166.52	H-Bond (Protein Donor)	false
O1G	N	HIS- 121	3.12	175.18	H-Bond (Protein Donor)	false
O2G	N	VAL- 123	3.03	160.65	H-Bond (Protein Donor)	false
O2G	N	GLY- 124	2.78	160.46	H-Bond (Protein Donor)	false
O1A	N	VAL- 125	3.1	132.62	H-Bond (Protein Donor)	false
O2A	N	VAL- 125	2.78	154.55	H-Bond (Protein Donor)	false
O2G	NE2	GLN- 370	2.88	154.46	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 372	2.8	158.29	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 372	2.8	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 372	3.61	0	Ionic (Protein Cationic)	false
O3G	MG	MG- 602	2.18	0	Metal Acceptor	false
O1B	MG	MG- 602	2.31	0	Metal Acceptor	false
O2A	MG	MG- 602	2.14	0	Metal Acceptor	false