scPDB - 3ntd entry

Protein Data Bank Entry:

PDB ID : 3ntd

Resolution :1.990 Å

Experimental Method : X-ray

Deposition Date : 2010-07-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FAD-dependent pyridine nucleotide-disulphide oxidoreductase
ID:	A3QAV3_SHELP
AC:	A3QAV3
Organism:	Shewanella loihica
Reign:	Bacteria
TaxID:	323850
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	29.966
Number of residues:	62
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:	COA
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.365	1265.625

% Hydrophobic	% Polar
47.73	52.27
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	75.69 %
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
9.29494	-46.424	26.2643

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
C4B	CG2	VAL- 10	3.98	0	Hydrophobic	false
C4'	CB	ALA- 11	3.85	0	Hydrophobic	false
O1P	N	GLY- 12	2.95	149.09	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 33	3	130.44	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 33	2.77	161.67	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 33	2.71	172.11	H-Bond (Ligand Donor)	false
N3A	N	ARG- 34	3.11	140.89	H-Bond (Protein Donor)	false
C2B	CD	ARG- 34	3.62	0	Hydrophobic	false
O2A	ND2	ASN- 42	3.18	160.49	H-Bond (Protein Donor)	false
C8	CB	ASN- 42	4.1	0	Hydrophobic	false
C6	CB	CYS- 43	4.43	0	Hydrophobic	false
C9A	SG	CYS- 43	3.96	0	Hydrophobic	false
C7M	CG	PRO- 46	4.28	0	Hydrophobic	false
N6A	O	VAL- 81	2.93	158.86	H-Bond (Ligand Donor)	false
N1A	N	VAL- 81	3.04	160.3	H-Bond (Protein Donor)	false
O1P	OG	SER- 112	2.89	137.44	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 133	3.71	0	Hydrophobic	false
O1A	NH2	ARG- 134	2.97	172.86	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 134	3.82	0	Ionic (Protein Cationic)	false
C1'	CZ	PHE- 161	4.48	0	Hydrophobic	false
C7	CG1	ILE- 162	3.66	0	Hydrophobic	false
C8	CD1	ILE- 162	3.65	0	Hydrophobic	false
O3'	OD1	ASP- 303	2.94	162.99	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 303	3.47	135.19	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 303	4.26	0	Hydrophobic	false
O2P	N	ASP- 303	2.73	165.73	H-Bond (Protein Donor)	false
N1	N	ALA- 321	3.46	127.85	H-Bond (Protein Donor)	false
O2	N	ALA- 321	2.89	176.09	H-Bond (Protein Donor)	false
C2'	CB	ALA- 321	3.93	0	Hydrophobic	false
C5'	CB	ALA- 324	4.18	0	Hydrophobic	false
N3	O	TYR- 446	2.82	164.82	H-Bond (Ligand Donor)	false
O1P	O	HOH- 575	2.64	179.94	H-Bond (Protein Donor)	false
O2P	O	HOH- 585	2.92	179.96	H-Bond (Protein Donor)	false
C2'	C2P	COA- 901	4.19	0	Hydrophobic	false