scPDB - 1u2d entry

Protein Data Bank Entry:

PDB ID : 1u2d

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2004-07-19

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	89 %
C	11 %

Ligand binding site composition:

B-Factor:	67.159
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.266	2446.875

% Hydrophobic	% Polar
47.03	52.97
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	67.64 %
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
-16.7995	-40.0246	22.396

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
C4N	CG	GLN- 132	4.05	0	Hydrophobic	false
C5N	CB	SER- 138	4.47	0	Hydrophobic	false
O1N	N	VAL- 182	2.88	158.84	H-Bond (Protein Donor)	false
C5N	CG2	VAL- 182	4.05	0	Hydrophobic	false
O3B	OD2	ASP- 202	3.23	150.35	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 202	2.96	139.12	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 202	2.7	150.86	H-Bond (Ligand Donor)	false
O3B	NE	ARG- 204	3.33	148.92	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 204	3.22	151.45	H-Bond (Protein Donor)	false
O2B	NE	ARG- 204	2.89	126.15	H-Bond (Protein Donor)	false
C2B	CD	ARG- 204	4.26	0	Hydrophobic	false
C5D	CD2	TYR- 235	4.16	0	Hydrophobic	false
C2B	CB	ALA- 236	3.64	0	Hydrophobic	false
C1B	CB	ALA- 265	4.32	0	Hydrophobic	false
C2D	C5N	NDP- 400	4.47	0	Hydrophobic	false
O7N	O2D	NDP- 400	2.86	146.28	H-Bond (Protein Donor)	false