scPDB - 2idx entry

Protein Data Bank Entry:

PDB ID : 2idx

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-09-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
ID:	MMAB_HUMAN
AC:	Q96EY8
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.17

Chains:

Chain Name:	Percentage of Residues within binding site
B	65 %
C	35 %

Ligand binding site composition:

B-Factor:	24.211
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.100	779.625

% Hydrophobic	% Polar
43.29	56.71
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	63.41 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
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
44.7649	44.9575	8.5759

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
O2G	N	THR- 60	2.8	162.67	H-Bond (Protein Donor)	false
O2G	OG1	THR- 60	2.61	160.37	H-Bond (Protein Donor)	false
O1G	N	GLY- 63	2.85	150.49	H-Bond (Protein Donor)	false
O1B	OG	SER- 68	2.64	158.35	H-Bond (Protein Donor)	false
C2'	CB	SER- 68	4.02	0	Hydrophobic	false
O2'	O	SER- 69	2.62	177.2	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 78	2.74	155.57	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 78	2.74	0	Ionic (Protein Cationic)	false
C2'	CE2	PHE- 83	3.43	0	Hydrophobic	false
O2A	CZ	ARG- 190	3.96	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 190	2.96	160.12	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 190	3.25	163.36	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 190	3.2	121.12	H-Bond (Protein Donor)	false
N6	O	ARG- 190	3.08	166.96	H-Bond (Ligand Donor)	false
N6	OE1	GLU- 193	3.05	145.8	H-Bond (Ligand Donor)	false
N1	NH1	ARG- 194	3.01	156.39	H-Bond (Protein Donor)	false
O1G	ND2	ASN- 214	2.87	158.48	H-Bond (Protein Donor)	false
O3G	ND2	ASN- 214	3.45	130	H-Bond (Protein Donor)	false
O2B	MG	MG- 604	1.9	0	Metal Acceptor	false
O2A	MG	MG- 604	1.97	0	Metal Acceptor	false
O1A	MG	MG- 605	2.25	0	Metal Acceptor	false
O1B	O	HOH- 630	2.91	179.98	H-Bond (Protein Donor)	false