scPDB - 3mvy entry

Protein Data Bank Entry:

PDB ID : 3mvy

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nickel-binding periplasmic protein
ID:	NIKA_ECOLI
AC:	P33590
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.568
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
0.316	941.625

% Hydrophobic	% Polar
40.14	59.86
According to VolSite

Ligand :

HET Code:	BHZ
Formula:	C20H23N2O5
Molecular weight:	371.407 g/mol
DrugBank ID:	-
Buried Surface Area:	55.05 %
Polar Surface area:	108.17 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
35.5176	22.2465	21.4148

Binding mode :

What is Poseview ?

2D View
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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
C19	CD2	TYR- 22	4.06	0	Hydrophobic	false
C15	SD	MET- 27	4.47	0	Hydrophobic	false
C21	SD	MET- 27	3.77	0	Hydrophobic	false
O21	NH1	ARG- 97	3.19	135.48	H-Bond (Protein Donor)	false
O21	NH2	ARG- 97	2.78	157.58	H-Bond (Protein Donor)	false
O21	CZ	ARG- 97	3.43	0	Ionic (Protein Cationic)	false
C19	CE2	TRP- 100	4.18	0	Hydrophobic	false
C21	CH2	TRP- 100	4.25	0	Hydrophobic	false
C10	CD2	TRP- 100	3.47	0	Hydrophobic	false
O22	NE	ARG- 137	3.32	135.31	H-Bond (Protein Donor)	false
O22	NH2	ARG- 137	2.81	158.99	H-Bond (Protein Donor)	false
O23	NE	ARG- 137	3	166.69	H-Bond (Protein Donor)	false
O22	CZ	ARG- 137	3.5	0	Ionic (Protein Cationic)	false
O23	CZ	ARG- 137	3.91	0	Ionic (Protein Cationic)	false
C12	CE2	TRP- 398	3.52	0	Hydrophobic	false
C9	CH2	TRP- 398	3.93	0	Hydrophobic	false
C14	CB	TRP- 398	3.74	0	Hydrophobic	false
C21	CE2	TYR- 402	4.34	0	Hydrophobic	false
C16	CG2	THR- 490	3.55	0	Hydrophobic	false
O6	FE	FE- 506	1.82	0	Metal Acceptor	false
O20	FE	FE- 506	2.24	0	Metal Acceptor	false
O22	FE	FE- 506	2.28	0	Metal Acceptor	false