scPDB - 1a59 entry

Protein Data Bank Entry:

PDB ID : 1a59

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 1998-02-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-methylcitrate synthase
ID:	PRPC_ABDS2
AC:	O34002
Organism:	Antarctic bacterium DS2-3R
Reign:	Bact
TaxID:	56673
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	13.164
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.051	931.500

% Hydrophobic	% Polar
37.32	62.68
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	46.58 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
-19.7348	60.9843	89.3673

Binding mode :

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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
C6P	CD1	LEU- 220	4.26	0	Hydrophobic	false
C6P	CB	ALA- 224	4.39	0	Hydrophobic	false
O2A	NZ	LYS- 263	2.61	153.06	H-Bond (Protein Donor)	false
O9P	NZ	LYS- 263	2.89	140.62	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 263	2.61	0	Ionic (Protein Cationic)	false
N1A	N	VAL- 264	2.94	164.7	H-Bond (Protein Donor)	false
N6A	O	VAL- 264	2.77	172.18	H-Bond (Ligand Donor)	false
C6P	CE	MET- 265	3.4	0	Hydrophobic	false
O5P	N	GLY- 266	2.83	159.23	H-Bond (Protein Donor)	false
N6A	O	PHE- 267	2.8	132.27	H-Bond (Ligand Donor)	false
N8P	O	PHE- 267	2.95	140.61	H-Bond (Ligand Donor)	false
O4A	NH2	ARG- 270	3.1	137.75	H-Bond (Protein Donor)	false
O4A	NE	ARG- 270	3.07	140.96	H-Bond (Protein Donor)	false
O4A	CZ	ARG- 270	3.49	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 273	3.77	0	Ionic (Protein Cationic)	false
C1B	CD1	ILE- 315	4.23	0	Hydrophobic	false
O5P	ND2	ASN- 318	3.09	167.88	H-Bond (Protein Donor)	false