scPDB - 2oo5 entry

Protein Data Bank Entry:

PDB ID : 2oo5

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2007-01-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P) transhydrogenase subunit alpha part 1
ID:	PNTAA_RHORT
AC:	Q2RSB2
Organism:	Rhodospirillum rubrum
Reign:	Bacteria
TaxID:	269796
EC Number:	1.6.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
B	85 %
C	15 %

Ligand binding site composition:

B-Factor:	31.213
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.340	2254.500

% Hydrophobic	% Polar
47.90	52.10
According to VolSite

Ligand :

HET Code:	TXD
Formula:	C21H30N7O14P2
Molecular weight:	666.449 g/mol
DrugBank ID:	-
Buried Surface Area:	70.02 %
Polar Surface area:	344.1 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
49.9358	45.4096	136.357

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
N7N	O	ARG- 127	3.36	138.11	H-Bond (Ligand Donor)	false
C4'A	CG	ARG- 127	4.46	0	Hydrophobic	false
O2N	CZ	ARG- 127	3.64	0	Ionic (Protein Cationic)	false
C4N	CG	GLN- 132	4.11	0	Hydrophobic	false
C5N	CB	SER- 138	4.49	0	Hydrophobic	false
C5N	CG2	VAL- 182	3.59	0	Hydrophobic	false
O1N	N	VAL- 182	2.95	169.81	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 202	2.71	162.25	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 202	3.15	159.61	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 202	2.56	129.66	H-Bond (Ligand Donor)	false
O3'	NH2	ARG- 204	3.31	149.83	H-Bond (Protein Donor)	false
O3'	NE	ARG- 204	3.41	148.38	H-Bond (Protein Donor)	false
O2'	NE	ARG- 204	3.15	127.6	H-Bond (Protein Donor)	false
O3'A	O	GLY- 234	2.65	162.38	H-Bond (Ligand Donor)	false
C5'A	CE2	TYR- 235	3.92	0	Hydrophobic	false
C2'	CB	ALA- 236	3.78	0	Hydrophobic	false
N1A	NE2	GLN- 247	3.07	177.42	H-Bond (Protein Donor)	false
C1'	CB	ALA- 265	4.16	0	Hydrophobic	false
O5'	N	LEU- 266	3.48	143.46	H-Bond (Protein Donor)	false
O7N	O2D	NAP- 400	2.91	163.04	H-Bond (Protein Donor)	false