scPDB - 2mjp entry

Protein Data Bank Entry:

PDB ID : 2mjp

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dITP/XTP pyrophosphatase
ID:	NTPA_METJA
AC:	Q57679
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	3.6.1.19

Chains:

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

Ligand binding site composition:

B-Factor:	6.551
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.828	1090.125

% Hydrophobic	% Polar
46.44	53.56
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	52.68 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
25.4598	11.7296	-1.04077

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
N3	ND2	ASN- 17	2.5	159.69	H-Bond (Protein Donor)	false
C1'	CB	ASN- 19	4.08	0	Hydrophobic	false
O3'	OE2	GLU- 23	3.03	156.64	H-Bond (Ligand Donor)	false
O2G	NZ	LYS- 90	2.75	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 90	3.78	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 90	3.27	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 90	3.27	144.29	H-Bond (Protein Donor)	false
C5'	CD2	PHE- 149	4.38	0	Hydrophobic	false
C1'	CE2	PHE- 149	4.42	0	Hydrophobic	false
O2B	NE2	HIS- 177	2.54	175.04	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 178	3.76	0	Ionic (Protein Cationic)	false
C3'	CD	ARG- 178	3.85	0	Hydrophobic	false