scPDB - 3ei8 entry

Protein Data Bank Entry:

PDB ID : 3ei8

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2008-09-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	LL-diaminopimelate aminotransferase, chloroplastic
ID:	DAPAT_ARATH
AC:	Q93ZN9
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	14 %
B	86 %

Ligand binding site composition:

B-Factor:	17.162
Number of residues:	55
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.589	502.875

% Hydrophobic	% Polar
45.64	54.36
According to VolSite

Ligand :

HET Code:	PL5
Formula:	C15H19N3O9P
Molecular weight:	416.300 g/mol
DrugBank ID:	-
Buried Surface Area:	80.26 %
Polar Surface area:	235.61 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-31.8062	60.4461	28.4909

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	OH	TYR- 37	2.97	156.43	H-Bond (Protein Donor)	false
CAM	CD2	PHE- 39	3.52	0	Hydrophobic	false
CB	CG	PHE- 39	3.71	0	Hydrophobic	false
CB	CG2	ILE- 63	3.66	0	Hydrophobic	false
OAD	N	GLY- 64	2.67	152.73	H-Bond (Protein Donor)	false
OAI	OH	TYR- 94	2.81	152.52	H-Bond (Protein Donor)	false
CAO	CE2	TYR- 94	3.59	0	Hydrophobic	false
CB	CE2	TYR- 94	4.3	0	Hydrophobic	false
N	OE2	GLU- 97	3.72	0	Ionic (Ligand Cationic)	false
OAJ	N	ALA- 128	2.85	157.02	H-Bond (Protein Donor)	false
CAP	CB	ALA- 128	4.49	0	Hydrophobic	false
OAE	N	LYS- 129	3	162.18	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 129	2.8	123.47	H-Bond (Protein Donor)	false
CAP	CB	LYS- 129	4.07	0	Hydrophobic	false
OXT	NZ	LYS- 129	2.8	0	Ionic (Protein Cationic)	false
CAP	CZ	TYR- 152	4.1	0	Hydrophobic	false
CAA	CG	TYR- 152	3.83	0	Hydrophobic	false
CAM	CE1	TYR- 152	4.43	0	Hydrophobic	false
O	OH	TYR- 152	2.72	155.66	H-Bond (Protein Donor)	false
CAA	SG	CYS- 205	3.53	0	Hydrophobic	false
CAA	CB	ASN- 209	4.07	0	Hydrophobic	false
OAH	ND2	ASN- 209	2.61	136.37	H-Bond (Protein Donor)	false
OAG	ND2	ASN- 209	2.79	146.65	H-Bond (Protein Donor)	false
NAR	OD2	ASP- 237	2.74	156.33	H-Bond (Protein Donor)	false
CAA	CB	ALA- 239	4.47	0	Hydrophobic	false
CAA	CE2	TYR- 240	4.04	0	Hydrophobic	false
OAH	OH	TYR- 240	2.96	152.36	H-Bond (Protein Donor)	false
OAJ	OG	SER- 267	2.5	154.55	H-Bond (Protein Donor)	false
OAI	OG	SER- 269	2.61	167.17	H-Bond (Protein Donor)	false
OAI	CZ	ARG- 278	3.71	0	Ionic (Protein Cationic)	false
OAE	CZ	ARG- 278	3.65	0	Ionic (Protein Cationic)	false
OAI	NH1	ARG- 278	2.93	169.3	H-Bond (Protein Donor)	false
OAE	NH2	ARG- 278	2.69	163.51	H-Bond (Protein Donor)	false
OAE	ND2	ASN- 309	2.9	153.64	H-Bond (Protein Donor)	false
O	ND2	ASN- 309	3.18	161.8	H-Bond (Protein Donor)	false
N	OD1	ASN- 309	2.77	161.17	H-Bond (Ligand Donor)	false
OAG	NH1	ARG- 404	2.88	173.77	H-Bond (Protein Donor)	false
OAD	NH1	ARG- 404	3.41	130.83	H-Bond (Protein Donor)	false
OAD	NH2	ARG- 404	2.81	161.31	H-Bond (Protein Donor)	false
OAG	CZ	ARG- 404	3.78	0	Ionic (Protein Cationic)	false
OAD	CZ	ARG- 404	3.54	0	Ionic (Protein Cationic)	false