scPDB - 2tmd entry

Protein Data Bank Entry:

PDB ID : 2tmd

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1993-10-15

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
B	100 %

Ligand binding site composition:

B-Factor:	14.963
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.312	489.375

% Hydrophobic	% Polar
36.55	63.45
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	68.53 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
2.70033	2.108	20.7115

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
O1B	OG	SER- 400	2.84	135.55	H-Bond (Protein Donor)	false
O1B	N	SER- 400	2.97	170.81	H-Bond (Protein Donor)	false
O2B	OG	SER- 400	3	143.9	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 419	3.15	144.35	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 419	2.82	147.88	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 419	2.79	161.58	H-Bond (Ligand Donor)	false
O2A	N	HIS- 427	2.86	171.03	H-Bond (Protein Donor)	false
O2A	ND1	HIS- 427	2.85	167.92	H-Bond (Protein Donor)	false
N6	O	MET- 470	3.23	161.25	H-Bond (Ligand Donor)	false
N1	N	MET- 470	2.98	159.44	H-Bond (Protein Donor)	false
O2B	N	ASP- 674	3	162.57	H-Bond (Protein Donor)	false
O1A	O	HOH- 816	2.82	157.94	H-Bond (Protein Donor)	false
O2B	O	HOH- 833	2.75	179.98	H-Bond (Protein Donor)	false
O1B	O	HOH- 860	2.75	179.96	H-Bond (Protein Donor)	false
O3'	O	HOH- 926	3.49	127.89	H-Bond (Protein Donor)	false