scPDB - 3zdf entry

Protein Data Bank Entry:

PDB ID : 3zdf

Resolution :2.340 Å

Experimental Method : X-ray

Deposition Date : 2012-11-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyceraldehyde-3-phosphate dehydrogenase
ID:	Q8DIW5_THEEB
AC:	Q8DIW5
Organism:	Thermosynechococcus elongatus
Reign:	Bacteria
TaxID:	197221
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	88 %
C	12 %

Ligand binding site composition:

B-Factor:	27.396
Number of residues:	53
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.153	1404.000

% Hydrophobic	% Polar
42.55	57.45
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.18 %
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
37.5642	-14.1763	4.936

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
O2A	N	ARG- 11	2.96	156.87	H-Bond (Protein Donor)	false
O1N	N	ILE- 12	2.8	177.05	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 12	3.51	0	Hydrophobic	false
O3B	OD1	ASP- 36	2.83	159.3	H-Bond (Ligand Donor)	false
O2B	OG1	THR- 37	3.12	159.4	H-Bond (Protein Donor)	false
C1B	CG2	THR- 37	4.36	0	Hydrophobic	false
C3D	CD1	TYR- 73	3.85	0	Hydrophobic	false
C2D	CG	TYR- 73	3.76	0	Hydrophobic	false
O1A	OH	TYR- 73	2.65	143.95	H-Bond (Protein Donor)	false
N6A	O	ARG- 81	3.04	170.54	H-Bond (Ligand Donor)	false
O4D	OG1	THR- 123	3.4	156.1	H-Bond (Protein Donor)	false
C5N	CB	CYS- 154	3.87	0	Hydrophobic	false
C4N	SG	CYS- 154	3.62	0	Hydrophobic	false
O7N	ND2	ASN- 317	2.83	174.28	H-Bond (Protein Donor)	false
C4N	CB	TYR- 321	4.49	0	Hydrophobic	false
N1A	O	HOH- 2002	2.83	179.96	H-Bond (Protein Donor)	false
O1N	O	HOH- 2003	2.61	175.42	H-Bond (Protein Donor)	false