scPDB - 1g63 entry

Protein Data Bank Entry:

PDB ID : 1g63

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2000-11-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Epidermin decarboxylase
ID:	EPID_STAEP
AC:	P30197
Organism:	Staphylococcus epidermidis
Reign:	Bacteria
TaxID:	1282
EC Number:	4.1.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
D	33 %
G	64 %

Ligand binding site composition:

B-Factor:	34.796
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.029	749.250

% Hydrophobic	% Polar
44.59	55.41
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	67.44 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
44.5887	7.13223	7.92

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
C2'	CB	ALA- 11	4.25	0	Hydrophobic	false
C5'	CB	ALA- 11	3.95	0	Hydrophobic	false
O2'	O	ALA- 11	2.81	164.79	H-Bond (Ligand Donor)	false
O2P	N	ALA- 11	2.59	163.4	H-Bond (Protein Donor)	false
N5	N	ILE- 13	3.41	140.8	H-Bond (Protein Donor)	false
C6	CB	ILE- 13	4.02	0	Hydrophobic	false
O2P	OG	SER- 37	2.9	171.95	H-Bond (Protein Donor)	false
C7M	CE2	PHE- 43	3.76	0	Hydrophobic	false
C8M	CZ	PHE- 43	4.05	0	Hydrophobic	false
C7M	CD1	LEU- 51	3.97	0	Hydrophobic	false
C7M	CD1	LEU- 64	3.68	0	Hydrophobic	false
C8M	CD1	LEU- 64	3.92	0	Hydrophobic	false
C5'	CB	SER- 83	4.4	0	Hydrophobic	false
O1P	OG	SER- 83	2.9	132.85	H-Bond (Protein Donor)	false
O2	N	ALA- 84	2.9	159.39	H-Bond (Protein Donor)	false
C5'	CB	ASN- 85	3.78	0	Hydrophobic	false
O5'	ND2	ASN- 85	3.46	125.19	H-Bond (Protein Donor)	false
O1P	ND2	ASN- 85	2.72	171.32	H-Bond (Protein Donor)	false
O1P	OG1	THR- 86	2.68	152.51	H-Bond (Protein Donor)	false
O3'	O	CYS- 95	2.95	159.32	H-Bond (Ligand Donor)	false
O4'	O	CYS- 95	3.1	168.6	H-Bond (Ligand Donor)	false
C1'	CG2	THR- 101	4.18	0	Hydrophobic	false
O3'	OG1	THR- 101	3.01	142.92	H-Bond (Protein Donor)	false
N3	O	ASN- 115	2.78	168.62	H-Bond (Ligand Donor)	false
O3P	O	HOH- 510	2.68	179.94	H-Bond (Protein Donor)	false