scPDB - 1kfb entry

Protein Data Bank Entry:

PDB ID : 1kfb

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2001-11-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan synthase alpha chain
ID:	TRPA_SALTY
AC:	P00929
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	17.093
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.543	735.750

% Hydrophobic	% Polar
48.62	51.38
According to VolSite

Ligand :

HET Code:	IGP
Formula:	C11H12NO6P
Molecular weight:	285.190 g/mol
DrugBank ID:	DB04143
Buried Surface Area:	64.16 %
Polar Surface area:	138.48 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
49.7735	27.1771	13.2017

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
C3	CG	PHE- 22	3.93	0	Hydrophobic	false
CH2	CB	ALA- 59	3.9	0	Hydrophobic	false
NE1	OD1	ASP- 60	3.01	145.55	H-Bond (Ligand Donor)	false
CD2	CG	LEU- 100	4	0	Hydrophobic	false
CE2	CD1	LEU- 100	3.56	0	Hydrophobic	false
CH2	CD2	LEU- 100	4.22	0	Hydrophobic	false
CH2	CB	ALA- 129	3.5	0	Hydrophobic	false
CZ3	CD1	ILE- 153	3.66	0	Hydrophobic	false
O3	OH	TYR- 175	2.93	168.32	H-Bond (Ligand Donor)	false
OP3	N	GLY- 213	2.74	169.14	H-Bond (Protein Donor)	false
C1	CG2	ILE- 232	4.41	0	Hydrophobic	false
OP2	N	GLY- 234	2.68	162.07	H-Bond (Protein Donor)	false
OP1	N	SER- 235	2.62	146.18	H-Bond (Protein Donor)	false
OP1	OG	SER- 235	2.69	156.69	H-Bond (Protein Donor)	false
OP2	N	SER- 235	3.22	137.95	H-Bond (Protein Donor)	false
OP2	O	HOH- 559	2.7	172.31	H-Bond (Protein Donor)	false