scPDB - 4dbc entry

Protein Data Bank Entry:

PDB ID : 4dbc

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aspartate aminotransferase
ID:	AAT_ECOLI
AC:	P00509
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.6.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	20.637
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.611	567.000

% Hydrophobic	% Polar
48.81	51.19
According to VolSite

Ligand :

HET Code:	3QP
Formula:	C13H12NO9P
Molecular weight:	357.209 g/mol
DrugBank ID:	-
Buried Surface Area:	70.82 %
Polar Surface area:	195.08 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-35.4587	24.2738	-6.48496

Binding mode :

What is Poseview ?

2D View
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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
C18	CG2	ILE- 45	4.03	0	Hydrophobic	false
O24	N	GLY- 46	2.78	156.51	H-Bond (Protein Donor)	false
O11	N	GLY- 115	2.73	153.9	H-Bond (Protein Donor)	false
O12	N	THR- 116	2.88	161.18	H-Bond (Protein Donor)	false
O12	OG1	THR- 116	2.76	152.02	H-Bond (Protein Donor)	false
C13	CD1	LEU- 119	4.24	0	Hydrophobic	false
C07	CH2	TRP- 142	3.75	0	Hydrophobic	false
C01	CB	TRP- 142	4.16	0	Hydrophobic	false
O21	NE1	TRP- 142	2.83	155.37	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 142	3.76	0	Aromatic Face/Face	false
C01	CB	ASN- 195	4.13	0	Hydrophobic	false
O04	ND2	ASN- 195	2.68	144.34	H-Bond (Protein Donor)	false
O23	ND2	ASN- 195	3.16	144.79	H-Bond (Protein Donor)	false
C02	CB	ALA- 225	4	0	Hydrophobic	false
C14	CB	ALA- 225	4.11	0	Hydrophobic	false
C01	CE2	TYR- 226	4.46	0	Hydrophobic	false
O11	OG	SER- 255	2.56	174.17	H-Bond (Protein Donor)	false
O11	OG	SER- 257	3.12	174.05	H-Bond (Protein Donor)	false
O10	NH1	ARG- 266	2.99	154.2	H-Bond (Protein Donor)	false
O12	NH2	ARG- 266	2.75	171.57	H-Bond (Protein Donor)	false
O10	CZ	ARG- 266	3.73	0	Ionic (Protein Cationic)	false
O12	CZ	ARG- 266	3.65	0	Ionic (Protein Cationic)	false
O23	NH1	ARG- 386	2.75	157.65	H-Bond (Protein Donor)	false
O24	NH2	ARG- 386	2.85	151.07	H-Bond (Protein Donor)	false
O23	CZ	ARG- 386	3.61	0	Ionic (Protein Cationic)	false
O24	CZ	ARG- 386	3.65	0	Ionic (Protein Cationic)	false