scPDB - 2ogi entry

Protein Data Bank Entry:

PDB ID : 2ogi

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2007-01-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q8DY32_STRA5
AC:	Q8DY32
Organism:	Streptococcus agalactiae serotype V
Reign:	Bacteria
TaxID:	208435
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.400
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	FE FE

Cavity properties

Ligandability	Volume (Å3)
0.519	725.625

% Hydrophobic	% Polar
46.05	53.95
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	61.7 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-8.13336	20.1627	62.4079

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
O1B	NZ	LYS- 62	3.02	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 62	2.72	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 62	2.72	170.51	H-Bond (Protein Donor)	false
C4'	CB	ASN- 88	3.97	0	Hydrophobic	false
C1'	CB	ASN- 88	4.07	0	Hydrophobic	false
N3	ND2	ASN- 88	3.48	142.64	H-Bond (Protein Donor)	false
O1A	OG1	THR- 118	2.76	159.9	H-Bond (Protein Donor)	false
C1'	CG2	THR- 118	4.28	0	Hydrophobic	false
C5'	CG2	THR- 118	3.98	0	Hydrophobic	false
O3B	CZ	ARG- 141	3.83	0	Ionic (Protein Cationic)	false
O3B	NH2	ARG- 141	2.82	147.51	H-Bond (Protein Donor)	false
O6	N	TYR- 180	2.93	150.8	H-Bond (Protein Donor)	false
O6	OG1	THR- 183	2.64	167.32	H-Bond (Protein Donor)	false
O3B	FE	FE- 301	2.33	0	Metal Acceptor	false
O2B	FE	FE- 302	2.18	0	Metal Acceptor	false
O1A	FE	FE- 302	2.12	0	Metal Acceptor	false