scPDB - 1yba entry

Protein Data Bank Entry:

PDB ID : 1yba

Resolution :2.240 Å

Experimental Method : X-ray

Deposition Date : 2004-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-3-phosphoglycerate dehydrogenase
ID:	SERA_ECOLI
AC:	P0A9T0
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.1.95

Chains:

Chain Name:	Percentage of Residues within binding site
C	2 %
D	98 %

Ligand binding site composition:

B-Factor:	44.336
Number of residues:	45
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.770	715.500

% Hydrophobic	% Polar
40.09	59.91
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	67.04 %
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
-20.0874	-48.6924	-25.0884

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	CG2	VAL- 112	3.72	0	Hydrophobic	false
O2A	N	HIS- 161	2.89	177	H-Bond (Protein Donor)	false
O2N	N	ILE- 162	2.91	176.48	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 162	4.31	0	Hydrophobic	false
C5N	CD1	ILE- 162	3.98	0	Hydrophobic	false
O3B	OD2	ASP- 181	2.65	144.75	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 181	3.33	128.44	H-Bond (Ligand Donor)	false
O3B	NZ	LYS- 185	2.79	172.33	H-Bond (Protein Donor)	false
C5D	CB	HIS- 210	4.45	0	Hydrophobic	false
O3D	O	VAL- 211	2.61	156.85	H-Bond (Ligand Donor)	false
N6A	OG	SER- 216	3.06	149.78	H-Bond (Ligand Donor)	false
N7N	O	ALA- 238	2.96	167.83	H-Bond (Ligand Donor)	false
C4D	CB	SER- 239	4.06	0	Hydrophobic	false
C3D	CG	ARG- 240	4.41	0	Hydrophobic	false
O3D	NE	ARG- 240	2.92	127.58	H-Bond (Protein Donor)	false
O2D	NH2	ARG- 240	3.32	135.55	H-Bond (Protein Donor)	false
O2D	NE	ARG- 240	3.07	149.42	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 264	3	175.49	H-Bond (Ligand Donor)	false
O7N	N	GLY- 295	3.16	142.57	H-Bond (Protein Donor)	false
O7N	O	HOH- 416	2.85	179.95	H-Bond (Protein Donor)	false
O2N	O	HOH- 417	2.81	165.12	H-Bond (Protein Donor)	false
N7A	O	HOH- 570	2.85	143.43	H-Bond (Protein Donor)	false