scPDB - 1dfo entry

Protein Data Bank Entry:

PDB ID : 1dfo

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1999-11-20

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_ECOLI
AC:	P0A825
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.2.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	22 %
B	78 %

Ligand binding site composition:

B-Factor:	29.074
Number of residues:	47
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.999	499.500

% Hydrophobic	% Polar
50.68	49.32
According to VolSite

Ligand :

HET Code:	PLG
Formula:	C10H13N2O7P
Molecular weight:	304.193 g/mol
DrugBank ID:	DB02824
Buried Surface Area:	80.95 %
Polar Surface area:	172.09 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
14.8091	97.6031	72.2009

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
OXT	OG	SER- 35	2.75	134.61	H-Bond (Protein Donor)	false
OXT	OH	TYR- 65	2.61	170.03	H-Bond (Protein Donor)	false
OP3	N	GLY- 98	3.28	172.2	H-Bond (Protein Donor)	false
OP1	N	SER- 99	3.01	154.91	H-Bond (Protein Donor)	false
OP1	OG	SER- 99	2.79	158.23	H-Bond (Protein Donor)	false
C2A	CB	HIS- 126	3.88	0	Hydrophobic	false
C3	CB	HIS- 126	4.26	0	Hydrophobic	false
DuAr	DuAr	HIS- 126	3.49	0	Aromatic Face/Face	false
O3	OG	SER- 175	2.81	167.95	H-Bond (Protein Donor)	false
N1	OD2	ASP- 200	2.6	144.88	H-Bond (Protein Donor)	false
C2A	CB	ASP- 200	4.49	0	Hydrophobic	false
C2A	CB	ALA- 202	3.85	0	Hydrophobic	false
C3	CB	ALA- 202	4.05	0	Hydrophobic	false
C5A	CG2	THR- 226	4.3	0	Hydrophobic	false
OP2	N	GLY- 263	2.96	179.75	H-Bond (Protein Donor)	false
O	CZ	ARG- 363	3.61	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 363	3.61	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 363	2.83	165.24	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 363	2.75	173.68	H-Bond (Protein Donor)	false
OP1	O	HOH- 506	2.97	179.95	H-Bond (Protein Donor)	false
OP3	O	HOH- 590	3.17	179.97	H-Bond (Protein Donor)	false