scPDB - 3wdl entry

Protein Data Bank Entry:

PDB ID : 3wdl

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-06-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-phosphopantoate--beta-alanine ligase
ID:	PPS_THEKO
AC:	Q5JIZ8
Organism:	Thermococcus kodakarensis )
Reign:	Archaea
TaxID:	69014
EC Number:	6.3.2.36

Chains:

Chain Name:	Percentage of Residues within binding site
A	94 %
B	6 %

Ligand binding site composition:

B-Factor:	28.212
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.070	1306.125

% Hydrophobic	% Polar
45.22	54.78
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	63.35 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
47.8337	-33.4316	22.5656

Binding mode :

What is Poseview ?

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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'	CB	ALA- 36	4.22	0	Hydrophobic	false
O1B	CZ	ARG- 39	3.85	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 39	3.07	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 39	3.08	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 39	3.2	135.52	H-Bond (Protein Donor)	false
C1'	CG	LEU- 161	4.06	0	Hydrophobic	false
O1G	N	GLY- 164	3.37	161.78	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 181	3.1	153.24	H-Bond (Ligand Donor)	false
N3	N	LEU- 182	3.4	145.34	H-Bond (Protein Donor)	false
O2'	N	ASN- 183	2.92	128.41	H-Bond (Protein Donor)	false
O3G	N	ARG- 187	3.22	169.64	H-Bond (Protein Donor)	false
O2G	N	SER- 188	3	170.28	H-Bond (Protein Donor)	false
N6	OD1	ASN- 199	3.5	139.36	H-Bond (Ligand Donor)	false
N1	N	ILE- 200	2.99	166.09	H-Bond (Protein Donor)	false