scPDB - 2gpj entry

Protein Data Bank Entry:

PDB ID : 2gpj

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Siderophore-interacting protein
ID:	A4Y1H9_SHEPC
AC:	A4Y1H9
Organism:	Shewanella putrefaciens
Reign:	Bacteria
TaxID:	319224
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.532
Number of residues:	53
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.222	1228.500

% Hydrophobic	% Polar
50.27	49.73
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	70.31 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
6.79302	31.3829	10.8633

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
C7M	CB	TYR- 43	4.12	0	Hydrophobic	false
O1A	CZ	ARG- 58	3.45	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 58	3.66	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 58	2.92	133.7	H-Bond (Protein Donor)	false
O1A	NE	ARG- 58	3.24	126.01	H-Bond (Protein Donor)	false
O1P	NE	ARG- 58	2.97	141.45	H-Bond (Protein Donor)	false
C9	CB	THR- 59	4.23	0	Hydrophobic	false
C7	CG2	THR- 59	3.46	0	Hydrophobic	false
C8	CG2	THR- 59	3.73	0	Hydrophobic	false
O2'	O	THR- 59	2.64	169.32	H-Bond (Ligand Donor)	false
C5'	CZ	TYR- 60	4.25	0	Hydrophobic	false
O4	N	THR- 61	3.04	153.95	H-Bond (Protein Donor)	false
N5	OG1	THR- 61	2.93	163.62	H-Bond (Protein Donor)	false
N3	O	ASP- 73	2.89	159.5	H-Bond (Ligand Donor)	false
O2	N	VAL- 75	2.89	169.6	H-Bond (Protein Donor)	false
O2P	NE2	HIS- 77	2.72	164.93	H-Bond (Protein Donor)	false
C4B	CG2	THR- 79	3.89	0	Hydrophobic	false
O1P	N	ALA- 83	2.87	164.7	H-Bond (Protein Donor)	false
O2P	N	SER- 84	3.16	157.62	H-Bond (Protein Donor)	false
C1'	CB	THR- 121	3.82	0	Hydrophobic	false
C7M	CE1	TYR- 225	3.66	0	Hydrophobic	false
C8M	CD1	TYR- 225	3.74	0	Hydrophobic	false
C1'	CB	TYR- 225	4.42	0	Hydrophobic	false
C9	CB	TYR- 225	3.75	0	Hydrophobic	false
DuAr	DuAr	TYR- 225	3.81	0	Aromatic Face/Face	false
C1B	CE3	TRP- 226	4.39	0	Hydrophobic	false
C3'	CB	TRP- 226	4.13	0	Hydrophobic	false
DuAr	DuAr	TRP- 226	3.43	0	Aromatic Face/Face	false
O2B	O	LYS- 227	2.86	121.93	H-Bond (Ligand Donor)	false
O2B	N	GLY- 229	3.46	123.33	H-Bond (Protein Donor)	false
O2B	O	CYS- 230	2.69	134.61	H-Bond (Ligand Donor)	false
C5B	CB	ASN- 231	4.44	0	Hydrophobic	false
O2A	N	GLU- 232	2.82	134.39	H-Bond (Protein Donor)	false
O4	O	HOH- 517	2.75	179.94	H-Bond (Protein Donor)	false