scPDB - 4a87 entry

Protein Data Bank Entry:

PDB ID : 4a87

Resolution :1.240 Å

Experimental Method : X-ray

Deposition Date : 2011-11-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Major pollen allergen Bet v 1-A
ID:	BEV1A_BETPN
AC:	P15494
Organism:	Betula pendula
Reign:	Eukaryota
TaxID:	3505
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.338
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
1.599	1096.875

% Hydrophobic	% Polar
63.08	36.92
According to VolSite

Ligand :

HET Code:	NAR
Formula:	C15H11O5
Molecular weight:	271.245 g/mol
DrugBank ID:	DB03467
Buried Surface Area:	66.06 %
Polar Surface area:	89.82 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
7.77655	2.9619	9.1094

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
C3	CG2	THR- 7	4.32	0	Hydrophobic	false
C2	CG2	THR- 9	4.14	0	Hydrophobic	false
C9	CZ	PHE- 22	4.37	0	Hydrophobic	false
C14	CD1	ILE- 23	3.34	0	Hydrophobic	false
C8	CZ	TYR- 83	4.45	0	Hydrophobic	false
C13	CD1	ILE- 102	4.02	0	Hydrophobic	false
C10	CD1	ILE- 102	3.48	0	Hydrophobic	false
C15	CG1	ILE- 102	3.84	0	Hydrophobic	false
C5	CG2	ILE- 116	3.96	0	Hydrophobic	false
C3	CD1	ILE- 116	3.68	0	Hydrophobic	false
O2	ND2	ASN- 118	3.17	157.54	H-Bond (Protein Donor)	false
C3	CG	LYS- 137	4.2	0	Hydrophobic	false