scPDB - 3oyz entry

Protein Data Bank Entry:

PDB ID : 3oyz

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2010-09-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate synthase
ID:	ACEB_HALVD
AC:	D4GTL2
Organism:	Haloferax volcanii
Reign:	Archaea
TaxID:	309800
EC Number:	2.3.3.9

Chains:

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

Ligand binding site composition:

B-Factor:	46.290
Number of residues:	47
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.166	489.375

% Hydrophobic	% Polar
63.45	36.55
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	54.53 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-31.4957	-4.51486	38.583

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
N6A	O	THR- 16	2.89	161.56	H-Bond (Ligand Donor)	false
O5P	OG1	THR- 16	2.82	169.83	H-Bond (Protein Donor)	false
C2P	CB	THR- 16	4.35	0	Hydrophobic	false
N1A	OG	SER- 17	2.82	157.27	H-Bond (Protein Donor)	false
C1B	CD	ARG- 33	3.91	0	Hydrophobic	false
O7A	CZ	ARG- 33	3.03	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 84	2.93	171.32	H-Bond (Protein Donor)	false
CH3	CG2	VAL- 191	3.93	0	Hydrophobic	false
S1P	CG	PRO- 231	4	0	Hydrophobic	false
CH3	CG	PRO- 231	3.86	0	Hydrophobic	false
CCP	CD1	ILE- 235	3.85	0	Hydrophobic	false
CEP	CD1	ILE- 235	3.95	0	Hydrophobic	false
O5A	NH1	ARG- 236	3.34	135.84	H-Bond (Protein Donor)	false
O5A	NH2	ARG- 236	2.86	165.07	H-Bond (Protein Donor)	false
O5A	CZ	ARG- 236	3.54	0	Ionic (Protein Cationic)	false
C2P	CZ2	TRP- 257	3.72	0	Hydrophobic	false
N6A	O	LEU- 259	3.09	138.08	H-Bond (Ligand Donor)	false
N8P	O	LEU- 259	2.99	142	H-Bond (Ligand Donor)	false
C6P	CD2	LEU- 259	4.17	0	Hydrophobic	false
C2P	CD2	LEU- 259	3.87	0	Hydrophobic	false
C1B	CG	PRO- 261	4.3	0	Hydrophobic	false
C6P	CB	ALA- 363	3.46	0	Hydrophobic	false
CEP	CG	MET- 386	3.53	0	Hydrophobic	false
C6P	CG	MET- 386	3.96	0	Hydrophobic	false
S1P	CE	MET- 386	3.65	0	Hydrophobic	false
CH3	CB	ALA- 390	4.3	0	Hydrophobic	false