scPDB - 1ytm entry

Protein Data Bank Entry:

PDB ID : 1ytm

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2005-02-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoenolpyruvate carboxykinase (ATP)
ID:	PCKA_ANASU
AC:	O09460
Organism:	Anaerobiospirillum succiniciproducens
Reign:	Bacteria
TaxID:	13335
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.378
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG MN

Cavity properties

Ligandability	Volume (Å3)
0.156	658.125

% Hydrophobic	% Polar
41.03	58.97
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	70.86 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
63.4545	24.9056	21.397

Binding mode :

What is Poseview ?

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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
O2G	N	GLY- 245	3.12	143.06	H-Bond (Protein Donor)	false
O3B	N	GLY- 245	2.55	142.82	H-Bond (Protein Donor)	false
O1B	N	THR- 246	3.38	123.46	H-Bond (Protein Donor)	false
O1B	N	GLY- 247	3.16	145.41	H-Bond (Protein Donor)	false
O3A	N	GLY- 247	3.41	147.39	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 248	2.75	164	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 248	2.76	157.71	H-Bond (Protein Donor)	false
O1B	N	LYS- 248	2.9	141.21	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 248	2.75	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 248	2.76	0	Ionic (Protein Cationic)	false
O2B	N	THR- 249	2.89	154.87	H-Bond (Protein Donor)	false
O1A	N	THR- 250	2.8	172.28	H-Bond (Protein Donor)	false
O1A	OG1	THR- 250	2.94	149.87	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 327	3.44	126.74	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 327	2.66	175.65	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 327	2.8	160.77	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 327	3.47	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 327	3.69	0	Ionic (Protein Cationic)	false
O4'	NH2	ARG- 443	3.07	120.41	H-Bond (Protein Donor)	false
N6	O	ILE- 444	3.06	162.19	H-Bond (Ligand Donor)	false
C2'	CD1	ILE- 446	4.34	0	Hydrophobic	false
N6	OG1	THR- 449	2.97	151.92	H-Bond (Ligand Donor)	false
O3G	MG	MG- 998	2.25	0	Metal Acceptor	false
O2B	MG	MG- 998	2.22	0	Metal Acceptor	false
O1G	MN	MN- 999	2.3	0	Metal Acceptor	false