scPDB - 3b1d entry

Protein Data Bank Entry:

PDB ID : 3b1d

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2011-06-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	BetaC-S lyase
ID:	A6BMJ3_STRAP
AC:	A6BMJ3
Organism:	Streptococcus anginosus
Reign:	Bacteria
TaxID:	1328
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	6 %
D	94 %

Ligand binding site composition:

B-Factor:	7.167
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.584	570.375

% Hydrophobic	% Polar
46.15	53.85
According to VolSite

Ligand :

HET Code:	PLS
Formula:	C11H15N2O8P
Molecular weight:	334.219 g/mol
DrugBank ID:	-
Buried Surface Area:	68.84 %
Polar Surface area:	192.32 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
6.68109	62.9865	117.174

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
CB	CG1	ILE- 34	4.1	0	Hydrophobic	false
O	N	ALA- 35	2.87	156.82	H-Bond (Protein Donor)	false
CA	CB	ALA- 35	3.57	0	Hydrophobic	false
CB	CE2	TYR- 60	3.62	0	Hydrophobic	false
O3P	OH	TYR- 60	2.65	171.47	H-Bond (Protein Donor)	false
O2P	N	VAL- 94	2.88	164.15	H-Bond (Protein Donor)	false
C5A	CG2	VAL- 95	4.17	0	Hydrophobic	false
O1P	N	VAL- 95	3.06	167.51	H-Bond (Protein Donor)	false
OG	OH	TYR- 119	2.82	164.44	H-Bond (Ligand Donor)	false
C2A	CD2	TYR- 119	3.8	0	Hydrophobic	false
C5A	CZ	TYR- 119	4.21	0	Hydrophobic	false
CA	CE1	TYR- 119	3.8	0	Hydrophobic	false
C2A	CE1	PHE- 122	4.24	0	Hydrophobic	false
C2A	SG	CYS- 167	3.37	0	Hydrophobic	false
OXT	ND2	ASN- 171	3.2	149.34	H-Bond (Protein Donor)	false
O3	ND2	ASN- 171	2.71	137.93	H-Bond (Protein Donor)	false
C2A	CB	ASN- 171	4.34	0	Hydrophobic	false
N1	OD2	ASP- 199	2.59	156.24	H-Bond (Protein Donor)	false
C2A	CG2	ILE- 201	4.09	0	Hydrophobic	false
C5A	CD1	ILE- 201	3.73	0	Hydrophobic	false
O3	NE2	HIS- 202	2.7	168.5	H-Bond (Protein Donor)	false
O	NH2	ARG- 365	2.93	170.35	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 365	3.34	131.45	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 365	2.75	163.75	H-Bond (Protein Donor)	false
O	CZ	ARG- 365	3.85	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 365	3.48	0	Ionic (Protein Cationic)	false