scPDB - 4tqo entry

Protein Data Bank Entry:

PDB ID : 4tqo

Resolution :2.570 Å

Experimental Method : X-ray

Deposition Date : 2014-06-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methanol dehydrogenase protein, large subunit
ID:	Q60AR6_METCA
AC:	Q60AR6
Organism:	Methylococcus capsulatus
Reign:	Bacteria
TaxID:	243233
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.451
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.699	617.625

% Hydrophobic	% Polar
43.17	56.83
According to VolSite

Ligand :

HET Code:	PQQ
Formula:	C14H3N2O8
Molecular weight:	327.182 g/mol
DrugBank ID:	DB03205
Buried Surface Area:	85.65 %
Polar Surface area:	183.21 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-1.71767	-70.2636	-104.848

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
O2B	OE1	GLU- 83	2.57	148.2	H-Bond (Protein Donor)	false
C9	SG	CYS- 131	3.89	0	Hydrophobic	false
C1A	SG	CYS- 132	3.56	0	Hydrophobic	false
C9A	SG	CYS- 132	3.73	0	Hydrophobic	false
O2B	NH1	ARG- 137	2.92	141.44	H-Bond (Protein Donor)	false
O9B	NH1	ARG- 137	3.2	155.29	H-Bond (Protein Donor)	false
O9A	OG1	THR- 187	2.63	175.08	H-Bond (Protein Donor)	false
C8	CB	ALA- 202	4.41	0	Hydrophobic	false
O7B	N	GLY- 203	2.62	163.85	H-Bond (Protein Donor)	false
O7A	N	ALA- 204	3.12	127.59	H-Bond (Protein Donor)	false
O7B	N	ALA- 204	2.99	169.71	H-Bond (Protein Donor)	false
O7B	OG1	THR- 269	2.78	145.93	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 271	3.73	0	Aromatic Face/Face	false
DuAr	DuAr	TRP- 271	3.69	0	Aromatic Face/Face	false
O5	NH2	ARG- 358	2.72	167.72	H-Bond (Protein Donor)	false
O5	NH1	ARG- 358	3.33	131.03	H-Bond (Protein Donor)	false
O2A	NE1	TRP- 497	3.49	131.39	H-Bond (Protein Donor)	false
O2A	N	TRP- 561	2.62	170.86	H-Bond (Protein Donor)	false
O5	CA	CA- 701	2.51	0	Metal Acceptor	false
N6	CA	CA- 701	2.75	0	Metal Acceptor	false