scPDB - 3pzc entry

Protein Data Bank Entry:

PDB ID : 3pzc

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2010-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Amino acid--[acyl-carrier-protein] ligase 1
ID:	AACL1_BRADU
AC:	Q89VT8
Organism:	Bradyrhizobium diazoefficiens
Reign:	Bacteria
TaxID:	224911
EC Number:	6.2.1.n2

Chains:

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

Ligand binding site composition:

B-Factor:	20.291
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.216	948.375

% Hydrophobic	% Polar
35.94	64.06
According to VolSite

Ligand :

HET Code:	GAP
Formula:	C12H17N6O8P
Molecular weight:	404.273 g/mol
DrugBank ID:	-
Buried Surface Area:	70.87 %
Polar Surface area:	232.41 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
93.5251	33.7349	5.58037

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
CA	CB	ALA- 129	4.17	0	Hydrophobic	false
O2A	NH1	ARG- 159	2.86	165.55	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 159	3.47	131.87	H-Bond (Protein Donor)	false
O3A	NH2	ARG- 159	2.74	160.94	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 159	3.6	0	Ionic (Protein Cationic)	false
N6	OE2	GLU- 161	3.13	150.04	H-Bond (Ligand Donor)	false
N6	O	LEU- 169	2.96	128.2	H-Bond (Ligand Donor)	false
N1	N	LEU- 169	3.04	166.14	H-Bond (Protein Donor)	false
C1'	CE1	PHE- 172	4.03	0	Hydrophobic	false
DuAr	DuAr	PHE- 172	3.66	0	Aromatic Face/Face	false
CA	SD	MET- 174	3.71	0	Hydrophobic	false
C5'	CE	MET- 174	3.84	0	Hydrophobic	false
O1A	NZ	LYS- 235	2.77	149.62	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 235	2.77	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 235	3.99	0	Ionic (Protein Cationic)	false
O2'	O	ALA- 250	3.04	148.44	H-Bond (Ligand Donor)	false
O1A	OG	SER- 253	2.62	162.93	H-Bond (Protein Donor)	false
CA	CB	ALA- 281	3.95	0	Hydrophobic	false
C5'	CB	ALA- 281	3.87	0	Hydrophobic	false
DuAr	CZ	ARG- 286	3.76	168.13	Pi/Cation	false
C2'	CD	ARG- 286	3.82	0	Hydrophobic	false
N3	O	HOH- 444	2.64	179.96	H-Bond (Protein Donor)	false