scPDB - 3klj entry

Protein Data Bank Entry:

PDB ID : 3klj

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2009-11-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH-rubredoxin oxidoreductase
ID:	NROR_CLOAB
AC:	Q9AL95
Organism:	Clostridium acetobutylicum
Reign:	Bacteria
TaxID:	272562
EC Number:	1.18.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	20.361
Number of residues:	58
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.329	1437.750

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	71.55 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-18.8696	-32.1834	-9.90617

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
C4'	CG	PRO- 13	4.29	0	Hydrophobic	false
O1P	N	ALA- 14	2.74	156.36	H-Bond (Protein Donor)	false
C1B	CB	SER- 34	4.46	0	Hydrophobic	false
N3A	N	SER- 34	3.42	131.73	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 35	2.78	159.61	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 42	3.96	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 42	3.42	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 42	3.32	128.8	H-Bond (Protein Donor)	false
O2A	NE	ARG- 42	2.67	167.16	H-Bond (Protein Donor)	false
C8M	CG	ARG- 42	3.85	0	Hydrophobic	false
C9A	CG	PRO- 43	4.04	0	Hydrophobic	false
C2'	CG	PRO- 43	3.86	0	Hydrophobic	false
C7M	CB	LEU- 45	4.48	0	Hydrophobic	false
N6A	O	ALA- 79	2.91	162.24	H-Bond (Ligand Donor)	false
N1A	N	ALA- 79	2.96	160.99	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 124	3.79	0	Hydrophobic	false
O1A	OH	TYR- 125	2.55	154.02	H-Bond (Protein Donor)	false
C8M	CD1	TYR- 125	4.09	0	Hydrophobic	false
C6	CD1	LEU- 151	4.35	0	Hydrophobic	false
C7M	CD1	LEU- 151	3.42	0	Hydrophobic	false
C7	CD2	LEU- 151	3.97	0	Hydrophobic	false
O3'	OD2	ASP- 259	2.82	173.09	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 259	4.04	0	Hydrophobic	false
O2P	N	ASP- 259	2.9	163.58	H-Bond (Protein Donor)	false
O2	N	ILE- 271	2.89	161.77	H-Bond (Protein Donor)	false
C2'	CB	ILE- 271	4.18	0	Hydrophobic	false
C4'	CG1	ILE- 271	4.35	0	Hydrophobic	false
C5'	CB	ALA- 274	3.79	0	Hydrophobic	false
O1P	O	HOH- 380	2.56	179.51	H-Bond (Protein Donor)	false
O2P	O	HOH- 391	2.63	179.97	H-Bond (Protein Donor)	false