scPDB - 1t57 entry

Protein Data Bank Entry:

PDB ID : 1t57

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2004-05-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Conserved protein
ID:	O27711_METTH
AC:	O27711
Organism:	Methanothermobacter thermautotrophicus
Reign:	Archaea
TaxID:	187420
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	75.258
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.414	556.875

% Hydrophobic	% Polar
38.79	61.21
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	73.09 %
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
-17.0079	-4.51871	-34.1633

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'	CB	ALA- 38	4.2	0	Hydrophobic	false
C8	CB	ALA- 38	4	0	Hydrophobic	false
C5'	CG1	VAL- 40	3.38	0	Hydrophobic	false
O5'	N	VAL- 40	2.95	136.67	H-Bond (Protein Donor)	false
O1P	OG	SER- 41	3.32	139.67	H-Bond (Protein Donor)	false
O2P	OG	SER- 41	3.08	150.07	H-Bond (Protein Donor)	false
O1P	N	THR- 44	3.31	144.34	H-Bond (Protein Donor)	false
O1P	OG1	THR- 44	3.18	154.28	H-Bond (Protein Donor)	false
O3P	OG1	THR- 44	3.06	133.38	H-Bond (Protein Donor)	false
C7M	CG1	VAL- 59	4.1	0	Hydrophobic	false
O4	NZ	LYS- 127	2.62	170.46	H-Bond (Protein Donor)	false
C6	CB	VAL- 128	4.42	0	Hydrophobic	false
C9A	CG1	VAL- 128	4.23	0	Hydrophobic	false
C7M	CG2	ILE- 132	3.57	0	Hydrophobic	false
C7M	CE	MET- 135	3.42	0	Hydrophobic	false
O2'	O	GLY- 153	3.12	170.23	H-Bond (Ligand Donor)	false
O2	N	ALA- 155	3.38	167.86	H-Bond (Protein Donor)	false
O3'	N	GLY- 157	3.45	136.59	H-Bond (Protein Donor)	false