scPDB - 1xp8 entry

Protein Data Bank Entry:

PDB ID : 1xp8

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2004-10-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein RecA
ID:	RECA_DEIRA
AC:	P42443
Organism:	Deinococcus radiodurans
Reign:	Bacteria
TaxID:	243230
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.712
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.337	523.125

% Hydrophobic	% Polar
42.58	57.42
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	57.83 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
21.0598	17.7505	3.48229

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
O3B	N	SER- 81	2.56	152.84	H-Bond (Protein Donor)	false
O1B	N	GLY- 83	2.61	154.11	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 84	3.98	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 84	3.06	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 84	3.06	159.3	H-Bond (Protein Donor)	false
O1B	N	LYS- 84	2.77	132.78	H-Bond (Protein Donor)	false
O3G	OG1	THR- 85	3.05	144.29	H-Bond (Protein Donor)	false
O2B	N	THR- 85	2.83	155	H-Bond (Protein Donor)	false
O2A	OG1	THR- 86	2.98	160.16	H-Bond (Protein Donor)	false
O2A	N	THR- 86	3.08	157.36	H-Bond (Protein Donor)	false
N6	OD1	ASP- 112	2.75	157.16	H-Bond (Ligand Donor)	false
C1'	CZ	TYR- 115	4	0	Hydrophobic	false
DuAr	DuAr	TYR- 115	3.69	0	Aromatic Face/Face	false
O3'	NZ	LYS- 239	2.76	147.19	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 275	3.89	0	Hydrophobic	false
C2'	CD1	TYR- 277	3.53	0	Hydrophobic	false
N3	N	GLY- 278	3.11	139.57	H-Bond (Protein Donor)	false