scPDB - 1p9w entry

Protein Data Bank Entry:

PDB ID : 1p9w

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2003-05-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Type II secretion system protein E
ID:	GSPE_VIBCH
AC:	P37093
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.924
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.317	864.000

% Hydrophobic	% Polar
35.94	64.06
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	53.43 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
29.4418	-20.7434	-140.652

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
C2'	CB	THR- 232	3.99	0	Hydrophobic	false
N6	O	LEU- 239	3.08	132.86	H-Bond (Ligand Donor)	false
O1G	N	GLY- 267	3.16	152.94	H-Bond (Protein Donor)	false
O1B	N	GLY- 269	3.06	132.3	H-Bond (Protein Donor)	false
O3A	N	GLY- 269	3.21	121.54	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 270	3.52	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 270	3.03	0	Ionic (Protein Cationic)	false
O1B	N	LYS- 270	3.12	164.71	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 270	3.03	152.71	H-Bond (Protein Donor)	false
O2B	N	SER- 271	2.76	143.58	H-Bond (Protein Donor)	false
O1A	N	THR- 272	2.95	128.66	H-Bond (Protein Donor)	false
O1A	OG1	THR- 272	3.08	152.03	H-Bond (Protein Donor)	false
C4'	CD1	LEU- 392	4.41	0	Hydrophobic	false
C1'	CD1	LEU- 392	4.08	0	Hydrophobic	false
O4'	NH2	ARG- 441	2.61	162.23	H-Bond (Protein Donor)	false