scPDB - 2bry entry

Protein Data Bank Entry:

PDB ID : 2bry

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2005-05-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	[F-actin]-methionine sulfoxide oxidase MICAL1
ID:	MICA1_MOUSE
AC:	Q8VDP3
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.14.13

Chains:

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

Ligand binding site composition:

B-Factor:	11.215
Number of residues:	59
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.501	1012.500

% Hydrophobic	% Polar
45.67	54.33
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	67.7 %
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
51.0168	30.1347	1.72575

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- 94	4.24	0	Hydrophobic	false
C5'	SG	CYS- 95	3.64	0	Hydrophobic	false
O1P	N	CYS- 95	3.01	162.62	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 114	2.65	167.14	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 114	3.16	125.37	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 114	2.65	165.48	H-Bond (Ligand Donor)	false
N3A	N	LYS- 115	3.2	140.32	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 116	2.64	149.14	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 121	3.36	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 121	2.94	144.54	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 121	2.92	145.68	H-Bond (Protein Donor)	false
C7	CD	ARG- 121	3.63	0	Hydrophobic	false
C8	CD	ARG- 121	3.66	0	Hydrophobic	false
N5	ND2	ASN- 123	3.01	165.67	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 125	3.9	0	Hydrophobic	false
C4'	CD1	LEU- 125	4.04	0	Hydrophobic	false
C6	CD1	ILE- 157	4.4	0	Hydrophobic	false
C9A	CD1	ILE- 157	3.98	0	Hydrophobic	false
C2'	CD1	ILE- 157	4.35	0	Hydrophobic	false
N6A	O	PHE- 181	2.94	161.5	H-Bond (Ligand Donor)	false
N1A	N	PHE- 181	2.99	159.91	H-Bond (Protein Donor)	false
N3	OH	TYR- 293	3.37	123.76	H-Bond (Ligand Donor)	false
O4	OH	TYR- 293	2.56	135.2	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 393	3.1	136.24	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 393	2.72	154.01	H-Bond (Ligand Donor)	false
O2P	N	ASP- 393	2.88	151.89	H-Bond (Protein Donor)	false
C1'	CE2	TRP- 400	4.01	0	Hydrophobic	false
C9A	CZ2	TRP- 400	3.37	0	Hydrophobic	false
O1P	O	HOH- 2453	2.77	179.97	H-Bond (Protein Donor)	false
N3	O	HOH- 2555	2.9	164.91	H-Bond (Ligand Donor)	false
O2A	O	HOH- 2686	2.66	179.97	H-Bond (Protein Donor)	false
O3B	O	HOH- 2820	2.72	131.81	H-Bond (Protein Donor)	false
O2P	O	HOH- 2822	2.71	179.99	H-Bond (Protein Donor)	false