scPDB - 1nkz entry

Protein Data Bank Entry:

PDB ID : 1nkz

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2003-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Light-harvesting protein B-800/850 alpha chain	Light-harvesting protein B-800/850 beta chain
ID:	LHA4_RHOAC	LHB5_RHOAC
AC:	P26789	P26790
Organism:	Rhodoblastus acidophilus
Reign:	Bacteria
TaxID:	1074
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	18 %
C	20 %
E	20 %
B	2 %
D	39 %

Ligand binding site composition:

B-Factor:	18.498
Number of residues:	52
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	8
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.785	1046.250

% Hydrophobic	% Polar
67.74	32.26
According to VolSite

Ligand :

HET Code:	RG1
Formula:	C46H66O6
Molecular weight:	715.013 g/mol
DrugBank ID:	-
Buried Surface Area:	44.54 %
Polar Surface area:	99.38 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
18.3472	17.5277	36.9331

Binding mode :

What is Poseview ?

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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
CM3	CB	GLN- 3	4.34	0	Hydrophobic	false
CM4	CG	GLN- 3	4.21	0	Hydrophobic	false
C6'	CD	LYS- 5	4.19	0	Hydrophobic	false
CM1	CD	LYS- 5	3.92	0	Hydrophobic	false
C2	CB	LYS- 5	4.32	0	Hydrophobic	false
O6'	NZ	LYS- 5	3.25	163.45	H-Bond (Protein Donor)	false
CM3	CB	ILE- 6	4.31	0	Hydrophobic	false
C2	CG1	VAL- 9	4.41	0	Hydrophobic	false
C4	CG2	VAL- 9	4.36	0	Hydrophobic	false
O2'	OE1	GLU- 10	2.88	174.83	H-Bond (Ligand Donor)	false
CM2	CB	GLU- 10	4.11	0	Hydrophobic	false
C4	CD1	LEU- 11	3.84	0	Hydrophobic	false
CM1	CE1	TYR- 14	3.98	0	Hydrophobic	false
CM2	CD1	TYR- 14	4.06	0	Hydrophobic	false
C3	CD1	TYR- 14	3.92	0	Hydrophobic	false
CM3	CD2	TYR- 14	3.57	0	Hydrophobic	false
CM6	CD1	LEU- 19	4.34	0	Hydrophobic	false
CM5	CD2	LEU- 20	3.97	0	Hydrophobic	false
CM5	CB	PHE- 22	4.35	0	Hydrophobic	false
CM6	CG2	VAL- 23	4.03	0	Hydrophobic	false
CM7	CD1	ILE- 26	4.08	0	Hydrophobic	false
CM8	CB	ALA- 27	3.72	0	Hydrophobic	false
CM8	CG1	ILE- 28	4.03	0	Hydrophobic	false
C28	CG1	ILE- 28	4.49	0	Hydrophobic	false
CM0	CB	LEU- 29	4.25	0	Hydrophobic	false
C28	CG2	VAL- 30	4.25	0	Hydrophobic	false
CM0	CG2	VAL- 30	3.92	0	Hydrophobic	false
CM9	CB	HIS- 31	4.43	0	Hydrophobic	false
C28	CB	HIS- 31	4.26	0	Hydrophobic	false
CM9	CD2	LEU- 32	4.11	0	Hydrophobic	false
CM0	CD2	LEU- 32	4.05	0	Hydrophobic	false
CM9	CB	ALA- 33	4.01	0	Hydrophobic	false
CM9	CH2	TRP- 45	3.67	0	Hydrophobic	false