scPDB - 4yvz entry

Protein Data Bank Entry:

PDB ID : 4yvz

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA integrity scanning protein DisA
ID:	DISA_THEMA
AC:	Q9WY43
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	17 %
B	83 %

Ligand binding site composition:

B-Factor:	40.754
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.516	1741.500

% Hydrophobic	% Polar
30.43	69.57
According to VolSite

Ligand :

HET Code:	3AT
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB01860
Buried Surface Area:	68.9 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.7174	-37.6578	40.3098

Binding mode :

What is Poseview ?

2D View
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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
O2'	N	GLY- 76	2.91	175.3	H-Bond (Protein Donor)	false
N6	O	LEU- 94	2.81	158.88	H-Bond (Ligand Donor)	false
N1	N	LEU- 94	3.11	157.63	H-Bond (Protein Donor)	false
O2A	N	THR- 107	3.45	142.75	H-Bond (Protein Donor)	false
O2A	OG1	THR- 107	2.73	157.42	H-Bond (Protein Donor)	false
O2G	NE	ARG- 108	3.08	146.71	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 108	3.13	141.47	H-Bond (Protein Donor)	false
O1B	N	ARG- 108	3.31	122.3	H-Bond (Protein Donor)	false
O3B	NE	ARG- 108	3.45	148.85	H-Bond (Protein Donor)	false
O3A	N	ARG- 108	3.03	163.16	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 108	3.54	0	Ionic (Protein Cationic)	false
C1'	CB	ARG- 108	4.39	0	Hydrophobic	false
O1B	ND1	HIS- 109	2.71	161.09	H-Bond (Protein Donor)	false
O1B	N	HIS- 109	3.34	158.46	H-Bond (Protein Donor)	false
O1G	OG	SER- 127	2.56	158.62	H-Bond (Protein Donor)	false
O2G	N	ARG- 128	2.86	151.93	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 130	2.58	159.96	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 130	3.61	0	Ionic (Protein Cationic)	false
O3G	MN	MN- 401	2.12	0	Metal Acceptor	false
O2B	MN	MN- 401	2.32	0	Metal Acceptor	false
O1A	MN	MN- 401	2.32	0	Metal Acceptor	false