scPDB - 3lgx entry

Protein Data Bank Entry:

PDB ID : 3lgx

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-01-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-alanine--poly(phosphoribitol) ligase subunit 1
ID:	DLTA_STRP1
AC:	Q99ZA6
Organism:	Streptococcus pyogenes serotype M1
Reign:	Bacteria
TaxID:	301447
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.150
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.706	1717.875

% Hydrophobic	% Polar
38.11	61.89
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	64.03 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
83.1449	114.754	-1.807

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
O2G	OG1	THR- 148	3.24	165.34	H-Bond (Protein Donor)	false
O2G	N	SER- 149	3.3	158.82	H-Bond (Protein Donor)	false
O3G	OG	SER- 149	3.17	124.68	H-Bond (Protein Donor)	false
O3G	N	SER- 149	3.13	128	H-Bond (Protein Donor)	false
O2B	N	SER- 149	3.22	124.52	H-Bond (Protein Donor)	false
N7	N	GLY- 268	2.95	137.88	H-Bond (Protein Donor)	false
N6	OD1	ASN- 290	3.21	144.18	H-Bond (Ligand Donor)	false
N6	O	ALA- 291	2.67	146.45	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 292	3.94	0	Hydrophobic	false
C5'	CB	PRO- 294	4.38	0	Hydrophobic	false
O1A	OG1	THR- 295	2.86	149.11	H-Bond (Protein Donor)	false
O1A	N	THR- 295	3.03	169	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 381	2.73	156.84	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 381	3.15	139.65	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 381	2.7	165.57	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 393	4.39	0	Hydrophobic	false
O1B	NZ	LYS- 495	3.86	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 495	3.18	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 495	3.18	166.35	H-Bond (Protein Donor)	false