scPDB - 3vax entry

Protein Data Bank Entry:

PDB ID : 3vax

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2011-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	A7TUX7_STRLI
AC:	A7TUX7
Organism:	Streptomyces lividans
Reign:	Bacteria
TaxID:	1916
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	93 %
B	7 %

Ligand binding site composition:

B-Factor:	15.996
Number of residues:	36
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.175	320.625

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	PLP
Formula:	C8H8NO6P
Molecular weight:	245.126 g/mol
DrugBank ID:	DB00114
Buried Surface Area:	65.34 %
Polar Surface area:	132.42 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
10.2194	-8.68673	24.2831

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
O1P	N	ALA- 69	3.06	162.14	H-Bond (Protein Donor)	false
C5A	CB	ALA- 69	3.94	0	Hydrophobic	false
O2P	N	THR- 70	2.88	158.2	H-Bond (Protein Donor)	false
O2P	OG1	THR- 70	2.68	156.23	H-Bond (Protein Donor)	false
C2A	CB	HIS- 99	3.77	0	Hydrophobic	false
C3	CB	HIS- 99	4.39	0	Hydrophobic	false
DuAr	DuAr	HIS- 99	3.6	0	Aromatic Face/Face	false
C2A	CE	MET- 146	3.97	0	Hydrophobic	false
C2A	CB	ASN- 150	4.11	0	Hydrophobic	false
C3	CB	ASN- 150	4.48	0	Hydrophobic	false
N1	OD1	ASP- 175	2.55	177.35	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 177	4.05	0	Hydrophobic	false
C3	CB	ALA- 177	3.76	0	Hydrophobic	false
O1P	OG	SER- 197	2.69	172.68	H-Bond (Protein Donor)	false
O3P	NE2	HIS- 199	2.85	166.14	H-Bond (Protein Donor)	false
C4A	CE	LYS- 200	3.48	0	Hydrophobic	false
O3P	OG1	THR- 242	3.4	131.7	H-Bond (Protein Donor)	false
O1P	O	HOH- 516	2.92	179.98	H-Bond (Protein Donor)	false