scPDB - 2jbl entry

Protein Data Bank Entry:

PDB ID : 2jbl

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2006-12-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Reaction center protein L chain
ID:	RCEL_BLAVI
AC:	P06009
Organism:	Blastochloris viridis
Reign:	Bacteria
TaxID:	1079
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
H	3 %
L	81 %
M	16 %

Ligand binding site composition:

B-Factor:	29.267
Number of residues:	42
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
1.464	411.750

% Hydrophobic	% Polar
75.41	24.59
According to VolSite

Ligand :

HET Code:	SMA
Formula:	C30H42O7
Molecular weight:	514.650 g/mol
DrugBank ID:	-
Buried Surface Area:	56.33 %
Polar Surface area:	83.45 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
129.319	68.6282	-3.47668

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
C21	CZ	PHE- 179	4.46	0	Hydrophobic	false
C25	CG1	VAL- 182	4.08	0	Hydrophobic	false
C23	CE	MET- 185	4.19	0	Hydrophobic	false
C25	SD	MET- 185	4.32	0	Hydrophobic	false
C25	CB	ALA- 186	4.28	0	Hydrophobic	false
C3M	CB	LEU- 189	3.51	0	Hydrophobic	false
C23	CD1	LEU- 189	3.76	0	Hydrophobic	false
C3M	CB	HIS- 190	4.01	0	Hydrophobic	false
O4	ND1	HIS- 190	2.58	149.01	H-Bond (Protein Donor)	false
O5	ND1	HIS- 190	3.18	130.84	H-Bond (Protein Donor)	false
C5M	CD2	LEU- 193	4.1	0	Hydrophobic	false
C5	CD2	LEU- 193	3.33	0	Hydrophobic	false
C5M	CD1	ILE- 194	3.74	0	Hydrophobic	false
C7M	CB	GLU- 212	3.94	0	Hydrophobic	false
C6	CB	GLU- 212	4.17	0	Hydrophobic	false
C3M	CZ	PHE- 216	4.27	0	Hydrophobic	false
C9	CE1	PHE- 216	3.66	0	Hydrophobic	false
C10	CD1	PHE- 216	4.18	0	Hydrophobic	false
C22	CG2	VAL- 220	3.96	0	Hydrophobic	false
C22	CD2	TYR- 222	3.71	0	Hydrophobic	false
O8	OG	SER- 223	2.63	157.11	H-Bond (Ligand Donor)	false
C8	CG2	ILE- 224	4.11	0	Hydrophobic	false
C10	CG2	ILE- 224	4.01	0	Hydrophobic	false
C24	CD1	ILE- 224	4.29	0	Hydrophobic	false
O8	N	GLY- 225	3.4	176	H-Bond (Protein Donor)	false
C5M	CB	ALA- 226	4.33	0	Hydrophobic	false
C6	CB	ALA- 226	4.44	0	Hydrophobic	false
C7M	CB	ALA- 226	4.26	0	Hydrophobic	false
C3M	CD1	ILE- 229	3.93	0	Hydrophobic	false
C5M	CG2	ILE- 229	4.25	0	Hydrophobic	false
C5	CG2	ILE- 229	3.94	0	Hydrophobic	false
C24	CD2	LEU- 232	3.69	0	Hydrophobic	false
C21	CE1	PHE- 235	4.22	0	Hydrophobic	false