scPDB - 2fjd entry

Protein Data Bank Entry:

PDB ID : 2fjd

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 2006-01-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylylsulfate reductase, subunit A (AprA)
ID:	O28603_ARCFU
AC:	O28603
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	11.097
Number of residues:	89
Including
Standard Amino Acids:	78
Non Standard Amino Acids:	0
Water Molecules:	11
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.688	421.875

% Hydrophobic	% Polar
44.80	55.20
According to VolSite

Ligand :

HET Code:	SFD
Formula:	C27H33N9O18P2S
Molecular weight:	865.613 g/mol
DrugBank ID:	-
Buried Surface Area:	81.25 %
Polar Surface area:	439.77 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	8
Rings:	6
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
29.3782	0.107825	131.346

Binding mode :

What is Poseview ?

2D View
3D View

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
C4R	CB	PHE- 32	4.34	0	Hydrophobic	false
OP3	N	PHE- 32	3.12	168.86	H-Bond (Protein Donor)	false
OP1	OG	SER- 33	2.67	150.49	H-Bond (Protein Donor)	false
OP1	N	SER- 33	2.88	163.28	H-Bond (Protein Donor)	false
O7R	OE1	GLU- 56	2.64	160.77	H-Bond (Ligand Donor)	false
O8R	OE1	GLU- 56	3.15	125.09	H-Bond (Ligand Donor)	false
O8R	OE2	GLU- 56	2.66	156.76	H-Bond (Ligand Donor)	false
N3A	N	LYS- 57	3.11	142.8	H-Bond (Protein Donor)	false
C8R	CB	SER- 63	4.17	0	Hydrophobic	false
O8R	OG	SER- 63	2.75	142.92	H-Bond (Protein Donor)	false
C2R	CB	ALA- 65	4.48	0	Hydrophobic	false
C3F	CB	ALA- 65	3.58	0	Hydrophobic	false
OP4	N	ALA- 65	2.93	164.72	H-Bond (Protein Donor)	false
C2R	CD1	LEU- 70	4.31	0	Hydrophobic	false
C6F	CD2	LEU- 70	3.69	0	Hydrophobic	false
N3F	O	ALA- 72	2.54	136.57	H-Bond (Ligand Donor)	false
O4F	O	ALA- 72	3.39	121.4	H-Bond (Ligand Donor)	false
O2F	N	ASN- 74	2.96	176.67	H-Bond (Protein Donor)	false
O1	ND2	ASN- 74	2.75	164.88	H-Bond (Protein Donor)	false
N1A	N	ILE- 176	3.11	167.17	H-Bond (Protein Donor)	false
N9	O	ILE- 176	2.84	163.93	H-Bond (Ligand Donor)	false
CAF	CE2	TRP- 234	4.24	0	Hydrophobic	false
C3F	CD1	TYR- 235	3.57	0	Hydrophobic	false
C3F	CB	ALA- 236	4.28	0	Hydrophobic	false
OP4	OD2	ASP- 239	2.71	176.18	H-Bond (Protein Donor)	false
N9	OG	SER- 242	2.89	166.13	H-Bond (Ligand Donor)	false
O2	NH2	ARG- 265	3.14	155.19	H-Bond (Protein Donor)	false
CBF	SD	MET- 365	4.2	0	Hydrophobic	false
O3R	OG	SER- 397	2.75	166.85	H-Bond (Ligand Donor)	false
C5R	CB	SER- 397	4.09	0	Hydrophobic	false
O2	NE2	HIS- 398	2.74	166.65	H-Bond (Protein Donor)	false
OP2	N	ASP- 439	2.85	167.18	H-Bond (Protein Donor)	false
C1R	CD2	PHE- 448	4.29	0	Hydrophobic	false
N1F	N	SER- 449	3.3	150.5	H-Bond (Protein Donor)	false
O2F	N	SER- 449	3.04	148.94	H-Bond (Protein Donor)	false
C5R	CB	SER- 452	3.95	0	Hydrophobic	false
C3F	CH2	TRP- 748	3.68	0	Hydrophobic	false
CAF	CZ2	TRP- 748	4.07	0	Hydrophobic	false
O7R	O	HOH- 5045	2.89	179.96	H-Bond (Protein Donor)	false
OP2	O	HOH- 5316	2.81	179.96	H-Bond (Protein Donor)	false
OP3	O	HOH- 5321	2.85	161.09	H-Bond (Protein Donor)	false
OP1	O	HOH- 5718	2.83	168.7	H-Bond (Protein Donor)	false
O3	O	HOH- 7587	3.05	179.96	H-Bond (Protein Donor)	false