scPDB - 1djq entry

Protein Data Bank Entry:

PDB ID : 1djq

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-12-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Trimethylamine dehydrogenase
ID:	DHTM_METME
AC:	P16099
Organism:	Methylophilus methylotrophus
Reign:	Bacteria
TaxID:	17
EC Number:	1.5.8.2

Chains:

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

Ligand binding site composition:

B-Factor:	16.732
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.155	303.750

% Hydrophobic	% Polar
66.67	33.33
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	84.34 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
36.5232	16.8293	-1.45374

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
C2'	CG2	VAL- 27	4.25	0	Hydrophobic	false
O2'	O	PRO- 28	2.58	137.21	H-Bond (Ligand Donor)	false
C2'	CB	HIS- 29	4.32	0	Hydrophobic	false
C8	CB	HIS- 29	3.7	0	Hydrophobic	false
N5	N	ALA- 30	2.89	162.11	H-Bond (Protein Donor)	false
C6	CB	ALA- 30	3.5	0	Hydrophobic	false
O4	N	TYR- 60	2.88	171.81	H-Bond (Protein Donor)	false
O2	OE2	GLU- 103	2.62	148.87	H-Bond (Protein Donor)	false
N3	OE1	GLU- 103	2.89	136.91	H-Bond (Ligand Donor)	false
N1	NH2	ARG- 222	2.94	123.02	H-Bond (Protein Donor)	false
O2	NH2	ARG- 222	2.67	129.01	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 222	3.22	132.41	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 222	2.97	141.16	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 222	2.69	144.83	H-Bond (Protein Donor)	false
C1'	CZ3	TRP- 264	3.56	0	Hydrophobic	false
C9A	CZ3	TRP- 264	3.36	0	Hydrophobic	false
O3'	OD1	ASP- 267	2.93	154.96	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 267	2.91	131.87	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 268	3.82	0	Hydrophobic	false
C5'	CG2	VAL- 297	3.42	0	Hydrophobic	false
O1P	N	ARG- 299	2.92	127.07	H-Bond (Protein Donor)	false
C8M	CB	ALA- 321	4.33	0	Hydrophobic	false
C9	CB	ALA- 321	4.49	0	Hydrophobic	false
C4'	CB	ALA- 321	4.2	0	Hydrophobic	false
C2'	CB	ALA- 321	3.82	0	Hydrophobic	false
O3P	N	ALA- 321	2.98	144.61	H-Bond (Protein Donor)	false
C8M	CG	ARG- 322	3.45	0	Hydrophobic	false
O1P	NH1	ARG- 322	2.85	175.64	H-Bond (Protein Donor)	false
O2P	NE	ARG- 322	2.81	160.08	H-Bond (Protein Donor)	false
O2P	N	ARG- 322	2.82	164.67	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 322	3.66	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 322	3.74	0	Ionic (Protein Cationic)	false
C7M	CD1	ILE- 325	4.48	0	Hydrophobic	false
C8M	CD1	ILE- 325	4.15	0	Hydrophobic	false
C7M	CB	CYS- 351	4.36	0	Hydrophobic	false
C8M	SG	CYS- 351	4.12	0	Hydrophobic	false
C7	CG1	ILE- 352	3.76	0	Hydrophobic	false
C8	CG1	ILE- 352	3.66	0	Hydrophobic	false
O3P	O	HOH- 810	2.65	164.16	H-Bond (Protein Donor)	false
O1P	O	HOH- 840	2.69	151.71	H-Bond (Protein Donor)	false