scPDB - 8atc entry

Protein Data Bank Entry:

PDB ID : 8atc

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1989-08-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aspartate carbamoyltransferase catalytic subunit
ID:	PYRB_ECOLI
AC:	P0A786
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	15.725
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.278	462.375

% Hydrophobic	% Polar
40.15	59.85
According to VolSite

Ligand :

HET Code:	PAL
Formula:	C6H6NO8P
Molecular weight:	251.088 g/mol
DrugBank ID:	DB03459
Buried Surface Area:	77.51 %
Polar Surface area:	182.36 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
68.1811	52.5578	62.6525

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
O3P	OG	SER- 52	2.65	156.95	H-Bond (Protein Donor)	false
O2P	N	THR- 53	2.97	153.76	H-Bond (Protein Donor)	false
O2P	N	ARG- 54	2.72	141.94	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 54	2.55	145.4	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 54	3.62	0	Ionic (Protein Cationic)	false
C1P	CD	ARG- 54	3.79	0	Hydrophobic	false
O3P	OG1	THR- 55	2.73	142.92	H-Bond (Protein Donor)	false
O3P	N	THR- 55	2.66	153.35	H-Bond (Protein Donor)	false
O1	OG1	THR- 55	2.91	122.39	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 105	3.02	147.51	H-Bond (Protein Donor)	false
O1	NH2	ARG- 105	2.88	169.74	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 105	3.59	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 105	3.63	0	Ionic (Protein Cationic)	false
O1	NE2	HIS- 134	2.73	170.72	H-Bond (Protein Donor)	false
O2	CZ	ARG- 167	3.54	0	Ionic (Protein Cationic)	false
O3	CZ	ARG- 167	3.63	0	Ionic (Protein Cationic)	false
O2	NH2	ARG- 167	2.74	170.45	H-Bond (Protein Donor)	false
O3	NE	ARG- 167	2.87	166.99	H-Bond (Protein Donor)	false
C3	CG2	THR- 168	3.7	0	Hydrophobic	false
O4	NH1	ARG- 229	3.06	161.65	H-Bond (Protein Donor)	false
O5	NH1	ARG- 229	2.72	124.69	H-Bond (Protein Donor)	false
O4	CZ	ARG- 229	3.69	0	Ionic (Protein Cationic)	false
O5	CZ	ARG- 229	3.77	0	Ionic (Protein Cationic)	false
C3	CG	PRO- 266	4.14	0	Hydrophobic	false
N2	O	LEU- 267	3.08	123.71	H-Bond (Ligand Donor)	false
O3	O	HOH- 330	2.5	179.96	H-Bond (Protein Donor)	false
O2	O	HOH- 367	3.21	179.96	H-Bond (Protein Donor)	false