scPDB - 3da1 entry

Protein Data Bank Entry:

PDB ID : 3da1

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-05-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycerol-3-phosphate dehydrogenase
ID:	Q9KDW6_BACHD
AC:	Q9KDW6
Organism:	Bacillus halodurans
Reign:	Bacteria
TaxID:	272558
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	41.912
Number of residues:	67
Including
Standard Amino Acids:	65
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.887	631.125

% Hydrophobic	% Polar
47.59	52.41
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.64 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
29.238	39.2361	81.3092

Binding mode :

What is Poseview ?

2D View
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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
C5'	CG2	ILE- 28	4.08	0	Hydrophobic	false
O5'	OG1	THR- 29	3.39	165.14	H-Bond (Protein Donor)	false
O1P	N	THR- 29	3.22	174.49	H-Bond (Protein Donor)	false
O2B	OE2	GLU- 48	2.8	160.12	H-Bond (Ligand Donor)	false
C2B	CE	MET- 49	4.05	0	Hydrophobic	false
C1B	CB	MET- 49	4.27	0	Hydrophobic	false
N3A	N	MET- 49	2.95	147.79	H-Bond (Protein Donor)	false
O3B	OG	SER- 54	2.87	143.59	H-Bond (Ligand Donor)	false
C8M	CG2	THR- 56	4.32	0	Hydrophobic	false
C9	CG2	THR- 56	4.08	0	Hydrophobic	false
C1'	CG2	THR- 56	4.13	0	Hydrophobic	false
C3'	CG2	THR- 56	4.02	0	Hydrophobic	false
O1A	OG	SER- 57	2.93	164.86	H-Bond (Protein Donor)	false
O1A	N	SER- 57	3.29	136.87	H-Bond (Protein Donor)	false
C1'	CB	SER- 60	3.98	0	Hydrophobic	false
C9A	CB	SER- 60	3.54	0	Hydrophobic	false
O4	OG1	THR- 61	2.93	149.69	H-Bond (Protein Donor)	false
N5	N	THR- 61	3.43	164.59	H-Bond (Protein Donor)	false
C6	CG2	THR- 61	3.56	0	Hydrophobic	false
N3	O	LEU- 63	3.05	142.11	H-Bond (Ligand Donor)	false
N6A	O	VAL- 193	3	153.39	H-Bond (Ligand Donor)	false
N1A	N	VAL- 193	3.08	159.26	H-Bond (Protein Donor)	false
C1B	CE3	TRP- 231	4.45	0	Hydrophobic	false
C3B	CZ3	TRP- 231	3.68	0	Hydrophobic	false
C7M	CG2	THR- 292	3.75	0	Hydrophobic	false
C8M	CB	ARG- 340	4.11	0	Hydrophobic	false
C2'	CB	LEU- 374	3.96	0	Hydrophobic	false
C4'	CB	LEU- 374	4.49	0	Hydrophobic	false
O2	OG1	THR- 375	3.16	143.34	H-Bond (Protein Donor)	false
O2P	O	HOH- 630	3.21	147.06	H-Bond (Protein Donor)	false