scPDB - 2pzj entry

Protein Data Bank Entry:

PDB ID : 2pzj

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative nucleotide sugar epimerase/ dehydratase
ID:	O87989_BORBO
AC:	O87989
Organism:	Bordetella bronchiseptica
Reign:	Bacteria
TaxID:	518
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.082
Number of residues:	54
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.841	756.000

% Hydrophobic	% Polar
33.04	66.96
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	80.3 %
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
20.0499	13.7803	16.1786

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
O2A	N	PHE- 23	2.89	172.81	H-Bond (Protein Donor)	false
O2N	N	VAL- 24	2.83	175.33	H-Bond (Protein Donor)	false
C5D	CB	VAL- 24	4.09	0	Hydrophobic	false
O3B	OD2	ASP- 44	2.72	160.53	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 44	3.32	127.36	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 44	3.32	128.41	H-Bond (Protein Donor)	false
O2B	OD1	ASP- 44	2.7	148.55	H-Bond (Protein Donor)	false
O2B	OD1	ASN- 45	3.38	169.65	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 45	3.41	128.96	H-Bond (Protein Donor)	false
O1A	OG	SER- 48	2.64	168.12	H-Bond (Protein Donor)	false
O2B	N	SER- 48	3.21	178.01	H-Bond (Protein Donor)	false
C2B	CB	SER- 48	4.31	0	Hydrophobic	false
C3B	CB	ALA- 49	3.98	0	Hydrophobic	false
N6A	OG	SER- 66	3.1	143.52	H-Bond (Ligand Donor)	false
N1A	N	ILE- 67	3.01	168.06	H-Bond (Protein Donor)	false
C4D	CB	LEU- 86	4.2	0	Hydrophobic	false
C1B	CB	ALA- 87	4.3	0	Hydrophobic	false
C5B	CG2	THR- 88	3.98	0	Hydrophobic	false
C3D	CG2	THR- 88	3.62	0	Hydrophobic	false
O2D	OG1	THR- 88	3.44	140.1	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 105	3.1	149.46	H-Bond (Ligand Donor)	false
O3D	OG	SER- 129	2.81	157.63	H-Bond (Ligand Donor)	false
C4D	CB	SER- 129	3.85	0	Hydrophobic	false
O2D	OH	TYR- 161	2.58	168.39	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 165	3.08	131.31	H-Bond (Protein Donor)	false
O7N	N	VAL- 191	3.01	153.45	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 191	4.18	0	Hydrophobic	false
O2A	NH2	ARG- 212	3.1	157.85	H-Bond (Protein Donor)	false
O5B	O	HOH- 363	3.05	161.26	H-Bond (Protein Donor)	false