scPDB - 1g1y entry

Protein Data Bank Entry:

PDB ID : 1g1y

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2000-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Neopullulanase 2
ID:	NEPU2_THEVU
AC:	Q08751
Organism:	Thermoactinomyces vulgaris
Reign:	Bacteria
TaxID:	2026
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	78 %
B	22 %

Ligand binding site composition:

B-Factor:	24.797
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.202	664.875

% Hydrophobic	% Polar
53.30	46.70
According to VolSite

Ligand :

HET Code:	BCD
Formula:	C42H70O35
Molecular weight:	1134.984 g/mol
DrugBank ID:	DB03995
Buried Surface Area:	31.4 %
Polar Surface area:	554.05 Å2

Number of
H-Bond Acceptors:	35
H-Bond Donors:	21
Rings:	9
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
36.632	56.8512	57.6877

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
O63	OH	TYR- 45	3.04	140.44	H-Bond (Protein Donor)	false
C62	CE2	TYR- 45	3.39	0	Hydrophobic	false
C14	CE1	TYR- 204	4.31	0	Hydrophobic	false
C24	CZ	TYR- 204	3.45	0	Hydrophobic	false
C34	CE2	TYR- 204	3.72	0	Hydrophobic	false
C44	CD2	TYR- 204	3.73	0	Hydrophobic	false
C15	CD2	TYR- 204	4.36	0	Hydrophobic	false
C63	CZ	PHE- 286	3.48	0	Hydrophobic	false
C64	CZ	PHE- 286	3.2	0	Hydrophobic	false
C64	CE	MET- 293	4.04	0	Hydrophobic	false
C65	CE	MET- 293	3.84	0	Hydrophobic	false
C63	CG2	VAL- 326	3.25	0	Hydrophobic	false
C33	CZ2	TRP- 356	4.12	0	Hydrophobic	false
C23	CE2	TRP- 356	3.24	0	Hydrophobic	false
O24	OD2	ASP- 421	2.89	132.43	H-Bond (Ligand Donor)	false
O25	OD2	ASP- 465	2.9	168.81	H-Bond (Ligand Donor)	false
O35	OD2	ASP- 465	2.7	149.6	H-Bond (Ligand Donor)	false
O25	NH2	ARG- 469	3.23	161.9	H-Bond (Protein Donor)	false
O25	NH1	ARG- 469	3.46	146.82	H-Bond (Protein Donor)	false