scPDB - 1bsv entry

Protein Data Bank Entry:

PDB ID : 1bsv

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1998-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-L-fucose synthase
ID:	FCL_ECOLI
AC:	P32055
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.932
Number of residues:	52
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.216	1177.875

% Hydrophobic	% Polar
42.41	57.59
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	58.57 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
29.2531	26.7475	12.2658

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
O2A	N	MET- 14	2.94	155.33	H-Bond (Protein Donor)	false
C3N	CE	MET- 14	3.96	0	Hydrophobic	false
O2N	N	VAL- 15	2.77	173.57	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 15	3.88	0	Hydrophobic	false
O3X	NE	ARG- 36	2.56	132.51	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 36	2.84	0	Ionic (Protein Cationic)	false
N6A	OD1	ASN- 40	3.14	151.48	H-Bond (Ligand Donor)	false
N1A	N	LEU- 41	3.16	165.41	H-Bond (Protein Donor)	false
C1B	CB	ALA- 63	4.38	0	Hydrophobic	false
C3D	CB	ALA- 64	4.13	0	Hydrophobic	false
C5D	CG2	VAL- 66	4.25	0	Hydrophobic	false
C3D	CG2	VAL- 66	3.68	0	Hydrophobic	false
C2D	CB	SER- 107	4.04	0	Hydrophobic	false
O3D	OH	TYR- 136	2.94	149.07	H-Bond (Protein Donor)	false
C2D	CZ	TYR- 136	4.34	0	Hydrophobic	false
O3D	NZ	LYS- 140	2.83	160.1	H-Bond (Protein Donor)	false
C3N	CD1	LEU- 166	3.78	0	Hydrophobic	false
O2N	O	HOH- 437	2.73	161.15	H-Bond (Protein Donor)	false
O1A	O	HOH- 484	2.67	171.33	H-Bond (Protein Donor)	false