scPDB - 3lsm entry

Protein Data Bank Entry:

PDB ID : 3lsm

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2010-02-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyranose 2-oxidase
ID:	Q7ZA32_TRAOC
AC:	Q7ZA32
Organism:	Trametes ochracea
Reign:	Eukaryota
TaxID:	230624
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.304
Number of residues:	77
Including
Standard Amino Acids:	67
Non Standard Amino Acids:	0
Water Molecules:	10
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.187	465.750

% Hydrophobic	% Polar
44.93	55.07
According to VolSite

Ligand :

HET Code:	SFD
Formula:	C27H33N9O18P2S
Molecular weight:	865.613 g/mol
DrugBank ID:	-
Buried Surface Area:	73.26 %
Polar Surface area:	439.77 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	8
Rings:	6
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-1.73937	14.6781	-27.733

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
C4R	CG	PRO- 56	3.98	0	Hydrophobic	false
OP1	N	ILE- 57	2.99	161.99	H-Bond (Protein Donor)	false
O7R	OD1	ASP- 76	2.65	155.05	H-Bond (Ligand Donor)	false
O8R	OD2	ASP- 76	2.67	166.55	H-Bond (Ligand Donor)	false
O8R	OD1	ASP- 76	3.49	129.46	H-Bond (Ligand Donor)	false
N3A	N	ILE- 77	3.14	147.54	H-Bond (Protein Donor)	false
C6R	CG2	ILE- 77	4.24	0	Hydrophobic	false
CAF	CD1	ILE- 107	3.94	0	Hydrophobic	false
C3F	CD2	LEU- 111	4.33	0	Hydrophobic	false
C1F	SD	MET- 164	4.16	0	Hydrophobic	false
C3F	CB	MET- 164	4.18	0	Hydrophobic	false
C1R	SD	MET- 164	4.49	0	Hydrophobic	false
C2R	CB	MET- 164	4.36	0	Hydrophobic	false
C3R	SD	MET- 164	4.36	0	Hydrophobic	false
OP3	N	MET- 164	2.86	145.24	H-Bond (Protein Donor)	false
C6F	CB	TRP- 168	3.64	0	Hydrophobic	false
O4F	OG1	THR- 169	2.73	170.95	H-Bond (Ligand Donor)	false
CBF	CG2	THR- 169	4.13	0	Hydrophobic	false
N3F	O	ALA- 171	2.8	161.8	H-Bond (Ligand Donor)	false
O4F	N	ALA- 171	2.88	150.46	H-Bond (Protein Donor)	false
N1A	N	CYS- 283	3.04	161.65	H-Bond (Protein Donor)	false
N9	O	CYS- 283	3.11	162.57	H-Bond (Ligand Donor)	false
O3	NH2	ARG- 472	3.13	134.32	H-Bond (Protein Donor)	false
O3	NH1	ARG- 472	2.69	158.83	H-Bond (Protein Donor)	false
O3	CZ	ARG- 472	3.35	0	Ionic (Protein Cationic)	false
C3F	CD1	LEU- 547	3.62	0	Hydrophobic	false
O2	NE2	HIS- 548	2.74	129.03	H-Bond (Protein Donor)	false
O1	ND2	ASN- 593	2.9	129.82	H-Bond (Protein Donor)	false
N1F	OG1	THR- 595	3.12	139.85	H-Bond (Protein Donor)	false
O2F	OG1	THR- 595	2.75	150.15	H-Bond (Protein Donor)	false
O2F	N	THR- 595	3.2	151.87	H-Bond (Protein Donor)	false
O3R	OG1	THR- 595	2.84	165.15	H-Bond (Ligand Donor)	false
C4R	CG2	THR- 595	4.11	0	Hydrophobic	false
O2F	O	HOH- 1001	2.88	179.98	H-Bond (Protein Donor)	false
OP1	O	HOH- 1057	2.73	179.95	H-Bond (Protein Donor)	false
N9	O	HOH- 1095	3.1	135.95	H-Bond (Ligand Donor)	false
N7A	O	HOH- 1132	3.01	179.98	H-Bond (Protein Donor)	false
OP2	O	HOH- 1137	2.82	150.8	H-Bond (Protein Donor)	false
OP4	O	HOH- 1171	2.7	179.96	H-Bond (Protein Donor)	false