scPDB - 3cis entry

Protein Data Bank Entry:

PDB ID : 3cis

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2008-03-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Universal stress protein Rv2623
ID:	Y2623_MYCTU
AC:	P9WFD7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	7 %
B	93 %

Ligand binding site composition:

B-Factor:	48.821
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:	ATP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.594	1886.625

% Hydrophobic	% Polar
41.14	58.86
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	76.59 %
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
-38.7503	17.8518	159.383

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
O3'	OG	SER- 17	3.43	172.07	H-Bond (Ligand Donor)	false
C2'	CB	ALA- 20	3.95	0	Hydrophobic	false
N6	O	ALA- 43	3.08	158.51	H-Bond (Ligand Donor)	false
N1	N	ALA- 43	3.12	162.56	H-Bond (Protein Donor)	false
C4'	CB	VAL- 116	4.26	0	Hydrophobic	false
C2'	CB	VAL- 116	4.43	0	Hydrophobic	false
C1'	CG1	VAL- 116	4.06	0	Hydrophobic	false
O2'	N	GLY- 117	2.72	161.23	H-Bond (Protein Donor)	false
O1B	N	GLY- 120	2.86	140.59	H-Bond (Protein Donor)	false
O3A	N	GLY- 120	2.84	120.91	H-Bond (Protein Donor)	false
O2B	N	GLY- 122	2.94	147.75	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 127	3.01	152.49	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 127	3.04	160.63	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 127	3.37	140.68	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 127	3.65	0	Ionic (Protein Cationic)	false
O1G	OG	SER- 131	3.32	130.95	H-Bond (Protein Donor)	false
O3G	OG	SER- 131	2.73	155.15	H-Bond (Protein Donor)	false
O3G	N	SER- 131	3.05	148.02	H-Bond (Protein Donor)	false
O1A	N	VAL- 132	2.8	137.28	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 132	3.97	0	Hydrophobic	false
O1A	N	SER- 133	3.36	157.58	H-Bond (Protein Donor)	false
O1G	MG	MG- 2001	2.38	0	Metal Acceptor	false
O2B	MG	MG- 2001	2.21	0	Metal Acceptor	false
O2A	MG	MG- 2001	2.55	0	Metal Acceptor	false