scPDB - 2zym entry

Protein Data Bank Entry:

PDB ID : 2zym

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2009-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Periplasmic binding protein
ID:	Q9AJF5_THEVU
AC:	Q9AJF5
Organism:	Thermoactinomyces vulgaris
Reign:	Bacteria
TaxID:	2026
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.237
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.754	837.000

% Hydrophobic	% Polar
46.37	53.63
According to VolSite

Ligand :

HET Code:	ACX
Formula:	C36H60O30
Molecular weight:	972.844 g/mol
DrugBank ID:	DB01909
Buried Surface Area:	55.83 %
Polar Surface area:	474.9 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	18
Rings:	8
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
20.2756	4.63352	15.9342

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
C2A	CB	ALA- 57	4.03	0	Hydrophobic	false
C2F	CB	LEU- 58	4.29	0	Hydrophobic	false
C3F	CD2	LEU- 58	4.05	0	Hydrophobic	false
C3A	CB	LEU- 59	3.79	0	Hydrophobic	false
C3B	CB	LEU- 59	4.06	0	Hydrophobic	false
C5B	CD1	LEU- 59	4.21	0	Hydrophobic	false
C3C	CB	LEU- 59	4	0	Hydrophobic	false
C3D	CD2	LEU- 59	3.89	0	Hydrophobic	false
C5E	CD1	LEU- 59	4.38	0	Hydrophobic	false
C3F	CG	LEU- 59	4.41	0	Hydrophobic	false
C5A	CD1	LEU- 59	4.35	0	Hydrophobic	false
O3A	N	LEU- 59	3.47	172.04	H-Bond (Protein Donor)	false
O3C	O	LEU- 59	2.58	130.44	H-Bond (Ligand Donor)	false
C3E	CG	PRO- 81	3.74	0	Hydrophobic	false
O2D	OD2	ASP- 83	3.39	129.68	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 83	2.62	171.56	H-Bond (Ligand Donor)	false
O3D	OD2	ASP- 83	2.86	174.01	H-Bond (Ligand Donor)	false
O3D	OD1	ASP- 83	3.48	123.21	H-Bond (Ligand Donor)	false
C2C	CD	ARG- 84	4.15	0	Hydrophobic	false
O2C	NH1	ARG- 84	2.86	159.81	H-Bond (Protein Donor)	false
O6D	ND2	ASN- 173	2.91	128.19	H-Bond (Protein Donor)	false
O6E	OD1	ASN- 173	3.05	168.43	H-Bond (Ligand Donor)	false
C1D	CD1	TYR- 175	3.57	0	Hydrophobic	false
C4E	CG	TYR- 175	3.92	0	Hydrophobic	false
C2E	CZ	TYR- 175	4.23	0	Hydrophobic	false
C6E	CD2	TYR- 175	3.73	0	Hydrophobic	false
C6E	CE1	TYR- 176	4	0	Hydrophobic	false
C6A	CB	ALA- 230	3.57	0	Hydrophobic	false
C1E	CH2	TRP- 250	3.71	0	Hydrophobic	false
C2E	CZ3	TRP- 250	3.86	0	Hydrophobic	false
C6F	CE2	TRP- 250	3.59	0	Hydrophobic	false
C2D	SD	MET- 350	4.06	0	Hydrophobic	false
C1C	CB	TRP- 360	3.8	0	Hydrophobic	false
C6C	CB	TRP- 360	4.48	0	Hydrophobic	false
C3D	CE2	TRP- 360	4.33	0	Hydrophobic	false
C6D	CE3	TRP- 360	3.48	0	Hydrophobic	false
C2D	CZ2	TRP- 360	3.83	0	Hydrophobic	false
C4D	CD2	TRP- 360	3.75	0	Hydrophobic	false
O6D	ND2	ASN- 364	3.22	151.22	H-Bond (Protein Donor)	false
O6F	O	HOH- 466	2.84	158.04	H-Bond (Ligand Donor)	false