scPDB - 5k8b entry

Protein Data Bank Entry:

PDB ID : 5k8b

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2016-05-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
ID:	KDNA_SHEON
AC:	Q8EEB1
Organism:	Shewanella oneidensis
Reign:	Bacteria
TaxID:	211586
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	82 %
D	18 %

Ligand binding site composition:

B-Factor:	16.576
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.974	1063.125

% Hydrophobic	% Polar
57.14	42.86
According to VolSite

Ligand :

HET Code:	PDG
Formula:	C13H16N2O9P
Molecular weight:	375.248 g/mol
DrugBank ID:	DB04762
Buried Surface Area:	74.56 %
Polar Surface area:	212.22 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-24.0533	-36.7432	16.5505

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
OP2	N	GLY- 61	2.89	144.61	H-Bond (Protein Donor)	false
OP1	N	THR- 62	2.92	152.21	H-Bond (Protein Donor)	false
OP1	OG1	THR- 62	2.59	160.64	H-Bond (Protein Donor)	false
C2A	CB	PHE- 87	4.4	0	Hydrophobic	false
C5A	CD1	PHE- 87	4.26	0	Hydrophobic	false
CGA	CE2	PHE- 87	3.64	0	Hydrophobic	false
C3	CB	PHE- 87	3.9	0	Hydrophobic	false
C5A	CB	ALA- 89	4.18	0	Hydrophobic	false
C2A	CG1	VAL- 131	3.63	0	Hydrophobic	false
C2A	SD	MET- 133	4.13	0	Hydrophobic	false
N1	OD2	ASP- 157	2.67	166.49	H-Bond (Ligand Donor)	false
C2A	CB	CYS- 159	4.13	0	Hydrophobic	false
C3	CB	CYS- 159	3.62	0	Hydrophobic	false
C2A	CG	GLN- 160	3.92	0	Hydrophobic	false
C3	CG	GLN- 160	4.39	0	Hydrophobic	false
O3	NE2	GLN- 160	2.66	167.15	H-Bond (Protein Donor)	false
C5A	CB	SER- 181	4.48	0	Hydrophobic	false
OP2	OG	SER- 181	2.62	166.58	H-Bond (Protein Donor)	false
OP3	OD1	ASP- 183	2.53	171.23	H-Bond (Protein Donor)	false
CBA	CG2	VAL- 185	4.5	0	Hydrophobic	false
CBA	CE	LYS- 186	4.23	0	Hydrophobic	false
C4	CE	LYS- 186	3.73	0	Hydrophobic	false
OE1	NH1	ARG- 222	3.31	126.85	H-Bond (Protein Donor)	false
OE1	NE	ARG- 222	2.65	159.72	H-Bond (Protein Donor)	false
OE2	NH1	ARG- 222	2.78	163.06	H-Bond (Protein Donor)	false
OE1	CZ	ARG- 222	3.4	0	Ionic (Protein Cationic)	false
OE2	CZ	ARG- 222	3.69	0	Ionic (Protein Cationic)	false
OP1	ND2	ASN- 233	2.9	166.8	H-Bond (Protein Donor)	false
OP3	NH2	ARG- 235	3.14	156.95	H-Bond (Protein Donor)	false
OA	NE2	HIS- 325	3.44	131	H-Bond (Protein Donor)	false
OXT	NE2	HIS- 325	2.66	165.72	H-Bond (Protein Donor)	false
OP2	O	HOH- 675	2.78	179.97	H-Bond (Protein Donor)	false