scPDB - 3kpb entry

Protein Data Bank Entry:

PDB ID : 3kpb

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2009-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein MJ0100
ID:	Y100_METJA
AC:	Q57564
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	88 %
D	12 %

Ligand binding site composition:

B-Factor:	17.290
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.540	1974.375

% Hydrophobic	% Polar
35.56	64.44
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	56.87 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
11.2866	10.2607	20.5985

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
N7	O	HOH- 17	3	179.97	H-Bond (Protein Donor)	false
O	OG1	THR- 436	2.94	160.09	H-Bond (Protein Donor)	false
OXT	OG1	THR- 436	3.4	144.36	H-Bond (Protein Donor)	false
C2'	CG2	THR- 436	4	0	Hydrophobic	false
C5'	CB	TRP- 438	4.33	0	Hydrophobic	false
C3'	CB	TRP- 438	4.31	0	Hydrophobic	false
O3'	OD1	ASP- 439	2.53	155.57	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 439	3.4	130.55	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 439	2.58	172.86	H-Bond (Ligand Donor)	false
O2'	OG1	THR- 456	2.67	162.69	H-Bond (Protein Donor)	false
N6	O	ILE- 460	3.16	173.91	H-Bond (Ligand Donor)	false
N1	N	ILE- 460	2.88	163.4	H-Bond (Protein Donor)	false
N	OG	SER- 481	3.23	142.32	H-Bond (Ligand Donor)	false
N6	O	GLY- 482	2.85	152.21	H-Bond (Ligand Donor)	false