scPDB - 3qbw entry

Protein Data Bank Entry:

PDB ID : 3qbw

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2011-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Anhydro-N-acetylmuramic acid kinase
ID:	ANMK_PSEAE
AC:	Q9I5Q5
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.825
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.373	540.000

% Hydrophobic	% Polar
46.88	53.13
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	62.71 %
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
37.0289	67.303	130.017

Binding mode :

What is Poseview ?

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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
O2B	N	SER- 12	3.34	139.31	H-Bond (Protein Donor)	false
O3B	N	SER- 12	3.32	140.68	H-Bond (Protein Donor)	false
O3B	OG	SER- 12	3.07	126.41	H-Bond (Protein Donor)	false
O3A	OG	SER- 12	3.36	164.99	H-Bond (Protein Donor)	false
C5'	CB	SER- 12	4.2	0	Hydrophobic	false
O3B	N	GLY- 165	3.18	167.66	H-Bond (Protein Donor)	false
C4'	CB	ASN- 187	4.41	0	Hydrophobic	false
C2'	CB	ASN- 187	4.39	0	Hydrophobic	false
O3'	OD2	ASP- 191	2.99	144.44	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 191	2.83	136.62	H-Bond (Ligand Donor)	false
C2'	CB	PHE- 202	3.52	0	Hydrophobic	false
N1	N	ASP- 205	2.74	148.7	H-Bond (Protein Donor)	false
O1A	N	GLY- 292	2.87	158.68	H-Bond (Protein Donor)	false
O5'	N	GLY- 292	3.32	122.72	H-Bond (Protein Donor)	false
O3B	O	HOH- 421	3.09	179.96	H-Bond (Protein Donor)	false