scPDB - 1xdy entry

Protein Data Bank Entry:

PDB ID : 1xdy

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-09-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein-methionine-sulfoxide reductase catalytic subunit MsrP
ID:	MSRP_ECOLI
AC:	P76342
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.156
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.417	415.125

% Hydrophobic	% Polar
49.59	50.41
According to VolSite

Ligand :

HET Code:	MTE
Formula:	C10H12N5O6PS2
Molecular weight:	393.336 g/mol
DrugBank ID:	-
Buried Surface Area:	79.35 %
Polar Surface area:	260.59 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
6.84933	68.533	36.4877

Binding mode :

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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
O1P	ND2	ASN- 44	3.15	163.96	H-Bond (Protein Donor)	false
C4'	CB	ASN- 45	4.3	0	Hydrophobic	false
O4	N	TYR- 47	3	154.55	H-Bond (Protein Donor)	false
N2	OE1	GLU- 48	2.69	165.57	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 48	3.25	132.5	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 48	2.61	152.47	H-Bond (Ligand Donor)	false
C4'	CE	MET- 100	4.42	0	Hydrophobic	false
N2	OG1	THR- 137	3.01	132.61	H-Bond (Ligand Donor)	false
O2P	ND2	ASN- 189	2.78	157.7	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 194	2.73	178.07	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 194	2.86	166.2	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 194	3.69	0	Ionic (Protein Cationic)	false
N8	O	GLY- 205	2.98	153.82	H-Bond (Ligand Donor)	false
N1	N	LYS- 207	3.06	162.92	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 207	2.71	163.75	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 207	2.71	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 207	3.65	0	Ionic (Protein Cationic)	false