scPDB - 3w5u entry

Protein Data Bank Entry:

PDB ID : 3w5u

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2013-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ferredoxin
ID:	Q9SLP6_MAIZE
AC:	Q9SLP6
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	83 %
H	17 %

Ligand binding site composition:

B-Factor:	20.530
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.845	594.000

% Hydrophobic	% Polar
44.89	55.11
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	52.5 %
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
16.7327	11.0898	44.3962

Binding mode :

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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
C8M	CB	SER- 38	3.95	0	Hydrophobic	false
C7M	CB	CYS- 39	4.2	0	Hydrophobic	false
C8M	SG	CYS- 44	3.99	0	Hydrophobic	false
O1A	NH2	ARG- 93	3.11	150.76	H-Bond (Protein Donor)	false
O2A	NE	ARG- 93	3.5	138.68	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 93	3.33	140.94	H-Bond (Protein Donor)	false
O1P	NE	ARG- 93	2.75	130.83	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 93	3.84	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 93	3.37	0	Ionic (Protein Cationic)	false
C3'	CG	ARG- 93	4.05	0	Hydrophobic	false
C7M	CD1	LEU- 94	4.23	0	Hydrophobic	false
C8	CB	LEU- 94	3.9	0	Hydrophobic	false
C2'	CE1	TYR- 95	3.78	0	Hydrophobic	false
C3'	CZ	TYR- 95	4.24	0	Hydrophobic	false
O4'	OH	TYR- 95	2.88	157.23	H-Bond (Ligand Donor)	false
O4	N	SER- 96	3.27	134.97	H-Bond (Protein Donor)	false
N5	N	SER- 96	3.23	152.36	H-Bond (Protein Donor)	false
N3	O	CYS- 114	2.83	161.13	H-Bond (Ligand Donor)	false
O2	N	LYS- 116	2.91	171.05	H-Bond (Protein Donor)	false
C5B	CD2	LEU- 118	3.94	0	Hydrophobic	false
C5'	CD2	LEU- 118	4.39	0	Hydrophobic	false
C1B	CZ	TYR- 120	3.93	0	Hydrophobic	false
DuAr	DuAr	TYR- 120	3.67	0	Aromatic Face/Face	false
O1A	N	VAL- 131	2.9	171.65	H-Bond (Protein Donor)	false
O3P	N	VAL- 131	3.43	126.19	H-Bond (Protein Donor)	false
O1P	N	CYS- 132	2.93	164.92	H-Bond (Protein Donor)	false
O2P	N	CYS- 132	3.19	122.5	H-Bond (Protein Donor)	false
O2P	N	SER- 133	2.84	160.56	H-Bond (Protein Donor)	false
O2P	OG	SER- 133	2.73	148.44	H-Bond (Protein Donor)	false
C7M	CG	GLU- 312	3.78	0	Hydrophobic	false
C1'	CD1	TYR- 314	3.71	0	Hydrophobic	false
C8	CB	TYR- 314	3.8	0	Hydrophobic	false
C9	CB	TYR- 314	3.66	0	Hydrophobic	false
DuAr	DuAr	TYR- 314	3.88	0	Aromatic Face/Face	false