scPDB - 1g5q entry

Protein Data Bank Entry:

PDB ID : 1g5q

Resolution :2.570 Å

Experimental Method : X-ray

Deposition Date : 2000-11-02

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	19 %
D	81 %

Ligand binding site composition:

B-Factor:	54.224
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	793.125

% Hydrophobic	% Polar
43.40	56.60
According to VolSite

Ligand :

HET Code:	ASP_SER_TYR_THR_CYS
Formula:	C23H32N5O11S
Molecular weight:	586.592 g/mol
DrugBank ID:	-
Buried Surface Area:	59.22 %
Polar Surface area:	323.78 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	9
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
225.401	74.0351	43.7968

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
CB	CG2	ILE- 13	3.68	0	Hydrophobic	false
CD1	CG1	ILE- 13	4.46	0	Hydrophobic	false
N	OD1	ASN- 14	2.84	141.52	H-Bond (Ligand Donor)	false
O	ND2	ASN- 14	3.05	157.51	H-Bond (Protein Donor)	false
CE1	CD1	ILE- 16	3.85	0	Hydrophobic	false
OH	ND2	ASN- 19	2.82	139.98	H-Bond (Protein Donor)	false
CE2	CG2	VAL- 23	4	0	Hydrophobic	false
CG2	CB	ASN- 117	4.4	0	Hydrophobic	false
OXT	ND2	ASN- 117	3.13	138.23	H-Bond (Protein Donor)	false
CB	CB	SER- 148	4.41	0	Hydrophobic	false
OG1	OG	SER- 148	2.83	161	H-Bond (Protein Donor)	false
O	N	PHE- 149	3.15	159.98	H-Bond (Protein Donor)	false
N	O	PHE- 149	3.11	137.15	H-Bond (Ligand Donor)	false
CD2	CB	PHE- 149	3.96	0	Hydrophobic	false
O	N	ILE- 151	2.91	138.55	H-Bond (Protein Donor)	false
SG	CD1	ILE- 151	4.14	0	Hydrophobic	false
O	N	SER- 152	2.79	125.84	H-Bond (Protein Donor)	false
OD1	OH	TYR- 156	3.13	133.48	H-Bond (Protein Donor)	false
CG2	CB	ASN- 159	4.27	0	Hydrophobic	false
CB	CB	THR- 161	3.71	0	Hydrophobic	false
CB	CG	MET- 162	4.39	0	Hydrophobic	false
OG	N	MET- 162	2.78	152.24	H-Bond (Protein Donor)	false
SG	C6	FMN- 301	3.36	0	Hydrophobic	false