scPDB - 2ggb entry

Protein Data Bank Entry:

PDB ID : 2ggb

Resolution :2.130 Å

Experimental Method : X-ray

Deposition Date : 2006-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine aminopeptidase
ID:	MAP1_ECOLI
AC:	P0AE18
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.986
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.572	378.000

% Hydrophobic	% Polar
45.54	54.46
According to VolSite

Ligand :

HET Code:	U17
Formula:	C17H34N3O6
Molecular weight:	376.468 g/mol
DrugBank ID:	-
Buried Surface Area:	57.16 %
Polar Surface area:	152.6 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
14.5128	-2.08942	18.0116

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
C15	CE2	TYR- 62	4.49	0	Hydrophobic	false
C18	CE2	TYR- 62	3.46	0	Hydrophobic	false
C18	CB	HIS- 63	3.79	0	Hydrophobic	false
C19	CB	HIS- 63	4.27	0	Hydrophobic	false
N1	OG1	THR- 99	3.02	156.5	H-Bond (Ligand Donor)	false
C13	CB	TYR- 168	4.46	0	Hydrophobic	false
C20	CE1	TYR- 168	3.75	0	Hydrophobic	false
O6	N	CYS- 169	3.16	170.87	H-Bond (Protein Donor)	false
C7	CZ	PHE- 177	3.68	0	Hydrophobic	false
O1	OE1	GLU- 204	2.56	170.2	H-Bond (Ligand Donor)	false
C18	CZ3	TRP- 221	3.92	0	Hydrophobic	false