scPDB - 3zl8 entry

Protein Data Bank Entry:

PDB ID : 3zl8

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2013-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
ID:	Q9WY78_THEMA
AC:	Q9WY78
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.365
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.774	975.375

% Hydrophobic	% Polar
35.64	64.36
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	73.14 %
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
1.73781	-3.83607	-23.9372

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
O3A	N	GLY- 92	2.83	151.09	H-Bond (Protein Donor)	false
O2B	N	LYS- 93	3.01	153.19	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 93	2.86	168.95	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 93	2.86	0	Ionic (Protein Cationic)	false
O1B	N	THR- 94	2.87	159.44	H-Bond (Protein Donor)	false
O1B	OG1	THR- 94	2.78	155.04	H-Bond (Protein Donor)	false
O2A	N	THR- 95	2.85	154.78	H-Bond (Protein Donor)	false
O2A	OG1	THR- 95	2.57	156.04	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 258	2.96	162.59	H-Bond (Protein Donor)	false
N7	ND2	ASN- 264	2.56	136.07	H-Bond (Protein Donor)	false
N6	OD1	ASN- 264	2.76	165.96	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 293	3.43	0	Ionic (Protein Cationic)	false
C5'	CG	ARG- 293	4.45	0	Hydrophobic	false
C3'	CB	ARG- 293	4.23	0	Hydrophobic	false
O2'	O	ARG- 293	2.8	123.98	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 307	2.53	176.03	H-Bond (Ligand Donor)	false
O3B	ND2	ASN- 310	3.06	122.53	H-Bond (Protein Donor)	false
C4'	CB	ALA- 315	4.15	0	Hydrophobic	false
C1'	CB	ALA- 315	4.46	0	Hydrophobic	false
O3'	NZ	LYS- 405	3.07	123.38	H-Bond (Protein Donor)	false