scPDB - 4b4d entry

Protein Data Bank Entry:

PDB ID : 4b4d

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-07-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ferredoxin-NADP reductase
ID:	Q8PMH0_XANAC
AC:	Q8PMH0
Organism:	Xanthomonas axonopodis pv. citri
Reign:	Bacteria
TaxID:	190486
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.922
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.553	590.625

% Hydrophobic	% Polar
45.71	54.29
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	69.83 %
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
21.3326	33.4774	23.9759

Binding mode :

What is Poseview ?

2D View
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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
C6	CB	PHE- 38	4.45	0	Hydrophobic	false
C7M	CD2	PHE- 38	3.71	0	Hydrophobic	false
C2'	CB	ARG- 52	4.09	0	Hydrophobic	false
C3'	CD	ARG- 52	3.9	0	Hydrophobic	false
O1P	NE	ARG- 52	2.95	127.64	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 52	3.07	123.99	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 52	3.36	0	Ionic (Protein Cationic)	false
O2'	O	ALA- 53	2.73	163.2	H-Bond (Ligand Donor)	false
C8	CB	ALA- 53	3.69	0	Hydrophobic	false
C2'	CE1	TYR- 54	4.22	0	Hydrophobic	false
C4'	CE1	TYR- 54	4.29	0	Hydrophobic	false
O4'	OH	TYR- 54	2.79	134.92	H-Bond (Ligand Donor)	false
O4	N	SER- 55	3.11	143.89	H-Bond (Protein Donor)	false
N5	N	SER- 55	3.29	141.9	H-Bond (Protein Donor)	false
N3	O	PHE- 68	2.84	178.61	H-Bond (Ligand Donor)	false
O2	N	ILE- 70	2.78	168.28	H-Bond (Protein Donor)	false
C5'	CG2	ILE- 70	3.89	0	Hydrophobic	false
C1B	CG2	VAL- 72	3.95	0	Hydrophobic	false
C5'	CG2	VAL- 72	4.41	0	Hydrophobic	false
C4B	CG1	VAL- 72	4.25	0	Hydrophobic	false
O1P	N	LEU- 77	2.88	168.63	H-Bond (Protein Donor)	false
O2P	N	THR- 78	2.84	164.07	H-Bond (Protein Donor)	false
O2P	OG1	THR- 78	2.73	141.27	H-Bond (Protein Donor)	false
C5'	CG2	THR- 78	3.72	0	Hydrophobic	false
N6A	OG1	THR- 118	2.91	175.08	H-Bond (Ligand Donor)	false
C7M	CG	GLU- 253	4.15	0	Hydrophobic	false
C7M	CG	ARG- 254	4.39	0	Hydrophobic	false
C8M	CG	ARG- 254	3.92	0	Hydrophobic	false
C1'	CB	PHE- 256	3.89	0	Hydrophobic	false
C2B	CD2	PHE- 256	3.92	0	Hydrophobic	false
DuAr	DuAr	PHE- 256	3.71	0	Aromatic Face/Face	false
O2B	OE1	GLU- 258	2.72	175.47	H-Bond (Ligand Donor)	false
O2A	NZ	LYS- 259	2.7	161.08	H-Bond (Protein Donor)	false
O3B	N	LYS- 259	2.88	162.84	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 259	2.7	0	Ionic (Protein Cationic)	false
O4	O	HOH- 2060	2.89	179.98	H-Bond (Protein Donor)	false