scPDB - 4wxg entry

Protein Data Bank Entry:

PDB ID : 4wxg

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2014-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine hydroxymethyltransferase
ID:	GLYA_STRT1
AC:	Q5M0B4
Organism:	Streptococcus thermophilus
Reign:	Bacteria
TaxID:	299768
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	24 %
C	76 %

Ligand binding site composition:

B-Factor:	33.398
Number of residues:	49
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.668	712.125

% Hydrophobic	% Polar
34.60	65.40
According to VolSite

Ligand :

HET Code:	2BO
Formula:	C12H17N2O8P
Molecular weight:	348.246 g/mol
DrugBank ID:	-
Buried Surface Area:	75.49 %
Polar Surface area:	192.32 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-11.7123	-64.4074	-11.6517

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
O	OG	SER- 29	2.77	146.38	H-Bond (Protein Donor)	false
O1P	OH	TYR- 49	2.59	161.33	H-Bond (Protein Donor)	false
O4P	OH	TYR- 49	3.39	126.85	H-Bond (Protein Donor)	false
OB	OE2	GLU- 51	2.79	125.52	H-Bond (Ligand Donor)	false
O	OH	TYR- 59	2.74	157.94	H-Bond (Protein Donor)	false
CG	CZ	TYR- 59	4.36	0	Hydrophobic	false
O2P	N	GLY- 92	2.93	157.85	H-Bond (Protein Donor)	false
O3P	OG	SER- 93	2.63	162.38	H-Bond (Protein Donor)	false
O3P	N	SER- 93	2.99	153.46	H-Bond (Protein Donor)	false
C2A	CB	HIS- 120	4.15	0	Hydrophobic	false
C3	CB	HIS- 120	4.35	0	Hydrophobic	false
DuAr	DuAr	HIS- 120	3.61	0	Aromatic Face/Face	false
O3	OG	SER- 170	2.73	156.58	H-Bond (Protein Donor)	false
N1	OD2	ASP- 195	2.64	141.99	H-Bond (Protein Donor)	false
C2A	CB	ALA- 197	3.86	0	Hydrophobic	false
C3	CB	ALA- 197	4.12	0	Hydrophobic	false
OT	NE2	HIS- 198	2.64	158.67	H-Bond (Protein Donor)	false
C5A	CG2	THR- 221	4.41	0	Hydrophobic	false
O2P	NE2	HIS- 223	3.29	166.85	H-Bond (Protein Donor)	false
O1P	N	GLY- 256	2.9	171.69	H-Bond (Protein Donor)	false
O	NH2	ARG- 357	3.06	176.92	H-Bond (Protein Donor)	false
OT	NH1	ARG- 357	2.87	168.17	H-Bond (Protein Donor)	false
O	CZ	ARG- 357	3.88	0	Ionic (Protein Cationic)	false
OT	CZ	ARG- 357	3.7	0	Ionic (Protein Cationic)	false
O3P	O	HOH- 622	2.74	179.98	H-Bond (Protein Donor)	false