scPDB - 5dg3 entry

Protein Data Bank Entry:

PDB ID : 5dg3

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-08-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
ID:	LPXA_PSEA7
AC:	A6V1E4
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	381754
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
B	46 %
E	2 %

Ligand binding site composition:

B-Factor:	26.818
Number of residues:	53
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	1140.750

% Hydrophobic	% Polar
51.48	48.52
According to VolSite

Ligand :

HET Code:	U21
Formula:	C27H43N3O19P2
Molecular weight:	775.587 g/mol
DrugBank ID:	-
Buried Surface Area:	59.84 %
Polar Surface area:	351.98 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
23.8293	-5.90882	33.5297

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
CBI	CG	PRO- 69	4.22	0	Hydrophobic	false
CAQ	CD1	LEU- 71	3.92	0	Hydrophobic	false
OAR	N	LEU- 71	2.96	163.44	H-Bond (Protein Donor)	false
O6	NZ	LYS- 72	3.04	129.69	H-Bond (Protein Donor)	false
CAQ	CD2	LEU- 112	4.33	0	Hydrophobic	false
CAQ	CE	MET- 114	3.92	0	Hydrophobic	false
CBI	SD	MET- 114	3.91	0	Hydrophobic	false
OBY	NE2	HIS- 118	3.07	149.81	H-Bond (Ligand Donor)	false
O4	NE2	HIS- 121	2.67	154.14	H-Bond (Ligand Donor)	false
CAQ	CD1	ILE- 130	3.82	0	Hydrophobic	false
CBS	CG1	VAL- 132	3.42	0	Hydrophobic	false
CBS	CG1	VAL- 132	3.42	0	Hydrophobic	false
CBS	CB	ASN- 133	3.85	0	Hydrophobic	false
CBV	CB	ALA- 136	3.68	0	Hydrophobic	false
CBX	CB	ALA- 138	3.81	0	Hydrophobic	false
CBS	CB	ALA- 138	4.33	0	Hydrophobic	false
O6	NE2	HIS- 140	2.94	170.48	H-Bond (Ligand Donor)	false
CBV	CD1	TYR- 152	3.94	0	Hydrophobic	false
CBX	CB	LEU- 154	4.15	0	Hydrophobic	false
O3'	NE2	HIS- 156	3.49	176.03	H-Bond (Ligand Donor)	false
OAV	NE2	GLN- 157	3.21	170.33	H-Bond (Protein Donor)	false
C6	CG	GLN- 157	4.22	0	Hydrophobic	false
C6	CE2	TYR- 158	3.99	0	Hydrophobic	false
C2'	CZ	PHE- 166	3.9	0	Hydrophobic	false
CBX	SD	MET- 169	4	0	Hydrophobic	false
OBQ	ND2	ASN- 194	3.36	147.22	H-Bond (Protein Donor)	false
NBM	OD1	ASN- 194	2.73	163.29	H-Bond (Ligand Donor)	false
OAT	NH1	ARG- 200	2.99	152.63	H-Bond (Protein Donor)	false
OAT	CZ	ARG- 200	3.75	0	Ionic (Protein Cationic)	false
OBT	O	HOH- 337	3.25	130.02	H-Bond (Protein Donor)	false
OBY	O	HOH- 414	2.97	179.96	H-Bond (Protein Donor)	false