scPDB - 4ymu entry

Protein Data Bank Entry:

PDB ID : 4ymu

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-03-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ABC-type polar amino acid transport system, ATPase component
ID:	Q8RCC2_CALS4
AC:	Q8RCC2
Organism:	Caldanaerobacter subterraneus subsp. tengcongensis
Reign:	Bacteria
TaxID:	273068
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
J	8 %

Ligand binding site composition:

B-Factor:	78.915
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.861	1096.875

% Hydrophobic	% Polar
28.00	72.00
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	48.05 %
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
-8.92239	10.1721	24.779

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
C1'	CD2	PHE- 11	4.12	0	Hydrophobic	false
DuAr	DuAr	PHE- 11	3.43	0	Aromatic Face/Face	false
C4'	CD1	LEU- 14	3.9	0	Hydrophobic	false
C1'	CD1	LEU- 14	4.1	0	Hydrophobic	false
C5'	CG1	VAL- 16	3.52	0	Hydrophobic	false
C4'	CG2	VAL- 16	3.68	0	Hydrophobic	false
C1'	CG2	VAL- 16	4.46	0	Hydrophobic	false
O3B	N	GLY- 37	2.94	169.03	H-Bond (Protein Donor)	false
O1B	N	GLY- 39	3.22	135.8	H-Bond (Protein Donor)	false
O3A	N	GLY- 39	3.41	146.86	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 40	2.84	145.91	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 40	2.65	137.3	H-Bond (Protein Donor)	false
O1B	N	LYS- 40	3.17	146.17	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 40	2.84	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 40	2.65	0	Ionic (Protein Cationic)	false
O2B	N	SER- 41	3.2	158.34	H-Bond (Protein Donor)	false
O2A	OG1	THR- 42	2.73	158.32	H-Bond (Protein Donor)	false
O2A	N	THR- 42	3.2	138.26	H-Bond (Protein Donor)	false
N6	OE1	GLU- 51	3.47	143.49	H-Bond (Ligand Donor)	false
O1G	NE2	HIS- 194	3.43	173.01	H-Bond (Protein Donor)	false
O3G	MG	MG- 302	2.43	0	Metal Acceptor	false
O1A	MG	MG- 302	2.69	0	Metal Acceptor	false