scPDB - 4isz entry

Protein Data Bank Entry:

PDB ID : 4isz

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-01-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA-splicing ligase RtcB
ID:	RTCB_PYRHO
AC:	O59245
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	6.5.1

Chains:

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

Ligand binding site composition:

B-Factor:	34.535
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.414	486.000

% Hydrophobic	% Polar
38.89	61.11
According to VolSite

Ligand :

HET Code:	GAV
Formula:	C10H12N5O13P3S
Molecular weight:	535.214 g/mol
DrugBank ID:	-
Buried Surface Area:	70.88 %
Polar Surface area:	332.4 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
37.4505	-5.04259	51.8018

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
C5'	CB	ASN- 202	3.82	0	Hydrophobic	false
N2	OE2	GLU- 206	2.6	157.66	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 206	3.05	127.77	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 206	2.57	153.01	H-Bond (Ligand Donor)	false
C1'	CG	PRO- 378	4.3	0	Hydrophobic	false
C4'	CG	PRO- 378	4.22	0	Hydrophobic	false
O2'	O	PRO- 378	3.31	149.52	H-Bond (Ligand Donor)	false
C2'	CB	SER- 380	4.25	0	Hydrophobic	false
N2	OG	SER- 385	3.45	137.99	H-Bond (Ligand Donor)	false
C2'	CB	ALA- 406	4.23	0	Hydrophobic	false
O2'	N	ALA- 406	3.06	139.56	H-Bond (Protein Donor)	false
O3'	N	ALA- 406	3.11	134.68	H-Bond (Protein Donor)	false
O3'	N	GLY- 407	2.75	167.91	H-Bond (Protein Donor)	false
C2'	CE2	TYR- 451	3.61	0	Hydrophobic	false
O6	NZ	LYS- 480	2.97	151.37	H-Bond (Protein Donor)	false
O2A	MN	MN- 502	2.26	0	Metal Acceptor	false
O3B	MN	MN- 502	2.65	0	Metal Acceptor	false
O1G	MN	MN- 503	2.52	0	Metal Acceptor	false