scPDB - 1nm5 entry

Protein Data Bank Entry:

PDB ID : 1nm5

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2003-01-09

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 beta
ID:	PNTB_RHORT
AC:	Q2RSB4
Organism:	Rhodospirillum rubrum
Reign:	Bacteria
TaxID:	269796
EC Number:	1.6.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
B	11 %
C	89 %

Ligand binding site composition:

B-Factor:	48.121
Number of residues:	47
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.926	1228.500

% Hydrophobic	% Polar
36.26	63.74
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	71.6 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-23.3023	-35.7268	7.8791

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
C5B	CB	TYR- 55	4.17	0	Hydrophobic	false
O2N	N	TYR- 55	3.15	155.48	H-Bond (Protein Donor)	false
C2D	CG2	VAL- 87	4.17	0	Hydrophobic	false
N7N	O	VAL- 87	3.32	120.31	H-Bond (Ligand Donor)	false
O2N	N	GLY- 89	3.34	168.36	H-Bond (Protein Donor)	false
N7N	O	GLY- 89	3.42	145.36	H-Bond (Ligand Donor)	false
O2A	NH2	ARG- 90	3.15	139.37	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 90	3.02	145.67	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 90	3.51	0	Ionic (Protein Cationic)	false
N7N	O	MET- 91	3.14	136.57	H-Bond (Ligand Donor)	false
O3B	ND2	ASN- 131	3.24	170.48	H-Bond (Protein Donor)	false
O1N	N	ASN- 131	2.83	167.8	H-Bond (Protein Donor)	false
C4B	CB	ASN- 131	4.17	0	Hydrophobic	false
O1A	N	ASP- 132	2.91	156.8	H-Bond (Protein Donor)	false
O3D	OD2	ASP- 132	2.75	152.05	H-Bond (Ligand Donor)	false
C3D	CB	ASP- 132	3.97	0	Hydrophobic	false
O1N	N	VAL- 133	3.23	162.56	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 164	2.96	126.76	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 164	3.46	165.85	H-Bond (Protein Donor)	false
C1B	CB	LYS- 164	4.17	0	Hydrophobic	false
O1X	NZ	LYS- 164	3.86	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 165	3.26	160.69	H-Bond (Protein Donor)	false
O2X	N	ARG- 165	2.67	158.85	H-Bond (Protein Donor)	false
O3X	NE	ARG- 165	3.4	136.63	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 165	2.94	157.87	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 165	3.6	0	Ionic (Protein Cationic)	false
O1X	OG	SER- 166	2.75	164.23	H-Bond (Protein Donor)	false
O1X	N	SER- 166	2.99	138.57	H-Bond (Protein Donor)	false
O3B	O	SER- 169	3.28	173.54	H-Bond (Ligand Donor)	false
C4D	CB	TYR- 171	3.73	0	Hydrophobic	false
N6A	OD1	ASP- 190	2.96	157.05	H-Bond (Ligand Donor)	false
N1A	N	ALA- 191	3.02	147.86	H-Bond (Protein Donor)	false