scPDB - 3m13 entry

Protein Data Bank Entry:

PDB ID : 3m13

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-03-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Monomeric sarcosine oxidase
ID:	MSOX_BACB0
AC:	P40859
Organism:	Bacillus sp.
Reign:	Bacteria
TaxID:	69000
EC Number:	1.5.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	35.798
Number of residues:	72
Including
Standard Amino Acids:	66
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.035	664.875

% Hydrophobic	% Polar
53.30	46.70
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	80.83 %
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
63.9242	-27.228	12.7819

Binding mode :

What is Poseview ?

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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
O1A	N	SER- 13	2.86	155.93	H-Bond (Protein Donor)	false
O1A	OG	SER- 13	2.77	167	H-Bond (Protein Donor)	false
O4'	OG	SER- 13	2.86	149.12	H-Bond (Ligand Donor)	false
C4'	CB	SER- 13	4.16	0	Hydrophobic	false
O2P	N	MET- 14	3.09	168.99	H-Bond (Protein Donor)	false
C5'	CE	MET- 14	4.23	0	Hydrophobic	false
O3B	OD1	ASP- 33	2.75	173.06	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 33	3.1	125.61	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 33	2.55	159.06	H-Bond (Ligand Donor)	false
N3A	N	ALA- 34	3.24	134.66	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 39	2.75	157.07	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 39	3.22	124.51	H-Bond (Protein Donor)	false
O2A	N	SER- 43	2.9	153.67	H-Bond (Protein Donor)	false
C5'	CB	SER- 43	3.91	0	Hydrophobic	false
O1A	ND1	HIS- 44	2.93	170.09	H-Bond (Protein Donor)	false
C6	CD	ARG- 49	4.32	0	Hydrophobic	false
C9A	CD	ARG- 49	3.74	0	Hydrophobic	false
C2'	CD	ARG- 49	4.45	0	Hydrophobic	false
O2'	NE	ARG- 49	2.87	164.62	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 49	3.76	170.62	Pi/Cation	false
N3	O	ILE- 50	2.86	142.24	H-Bond (Ligand Donor)	false
O4	N	ILE- 50	2.89	173.96	H-Bond (Protein Donor)	false
N6A	O	VAL- 173	2.9	161.7	H-Bond (Ligand Donor)	false
N1A	N	VAL- 173	2.87	168.28	H-Bond (Protein Donor)	false
C2B	CZ3	TRP- 204	4.16	0	Hydrophobic	false
C7M	CB	GLN- 223	4.31	0	Hydrophobic	false
C8M	CB	GLN- 223	4.31	0	Hydrophobic	false
C7M	CG2	VAL- 225	3.63	0	Hydrophobic	false
C7M	CZ	TYR- 254	4.31	0	Hydrophobic	false
C7M	CB	CYS- 315	3.4	0	Hydrophobic	false
C9	SG	CYS- 315	4.01	0	Hydrophobic	false
C8	SG	CYS- 315	3.67	0	Hydrophobic	false
C7M	CE1	TYR- 317	4.35	0	Hydrophobic	false
C8	CE1	TYR- 317	3.24	0	Hydrophobic	false
C5'	CB	PHE- 342	4.25	0	Hydrophobic	false
O3'	N	GLY- 346	3.26	150.58	H-Bond (Protein Donor)	false
N1	N	PHE- 347	3.13	150.34	H-Bond (Protein Donor)	false
C2'	CB	PHE- 347	3.61	0	Hydrophobic	false
O2	N	LYS- 348	3	157.38	H-Bond (Protein Donor)	false
O2A	O	HOH- 396	2.81	179.99	H-Bond (Protein Donor)	false
O1P	O	HOH- 410	2.64	135.34	H-Bond (Protein Donor)	false
O2P	O	HOH- 459	2.75	173.08	H-Bond (Protein Donor)	false