scPDB - 3abi entry

Protein Data Bank Entry:

PDB ID : 3abi

Resolution :2.440 Å

Experimental Method : X-ray

Deposition Date : 2009-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	O59312_PYRHO
AC:	O59312
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.910
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.062	860.625

% Hydrophobic	% Polar
48.63	51.37
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	69.29 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-0.418523	12.3048	128.164

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
O2N	N	ILE- 11	2.95	154.81	H-Bond (Protein Donor)	false
C5N	CG1	ILE- 11	4.18	0	Hydrophobic	false
O3B	OD2	ASP- 29	2.63	155.7	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 29	3.41	156.43	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 29	2.89	146.66	H-Bond (Ligand Donor)	false
N3A	N	VAL- 30	3.2	135.78	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 34	2.89	138.08	H-Bond (Protein Donor)	false
N6A	OD2	ASP- 48	3.01	173.09	H-Bond (Ligand Donor)	false
N1A	N	ALA- 49	3.15	159.31	H-Bond (Protein Donor)	false
C1B	CD2	LEU- 69	4.48	0	Hydrophobic	false
O3D	O	LEU- 69	2.67	143.48	H-Bond (Ligand Donor)	false
C5B	CG	PRO- 70	3.7	0	Hydrophobic	false
C4D	CG1	VAL- 91	4.05	0	Hydrophobic	false
C4D	CB	SER- 92	4.25	0	Hydrophobic	false
O3D	N	PHE- 93	2.74	152.97	H-Bond (Protein Donor)	false
O2D	N	PHE- 93	3.4	138.93	H-Bond (Protein Donor)	false
C2D	CB	PHE- 93	4.31	0	Hydrophobic	false
O7N	N	ALA- 119	3.13	165.57	H-Bond (Protein Donor)	false
N7N	O	PRO- 120	2.99	152.41	H-Bond (Ligand Donor)	false
C5N	CB	TRP- 160	3.66	0	Hydrophobic	false
O1N	N	SER- 161	3.11	141.73	H-Bond (Protein Donor)	false
O2D	OD2	ASP- 164	2.9	158.35	H-Bond (Ligand Donor)	false
C4N	SD	MET- 295	3.92	0	Hydrophobic	false
C4N	CG2	THR- 299	3.77	0	Hydrophobic	false
O2N	O	HOH- 2036	2.69	179.97	H-Bond (Protein Donor)	false