scPDB - 2dph entry

Protein Data Bank Entry:

PDB ID : 2dph

Resolution :2.270 Å

Experimental Method : X-ray

Deposition Date : 2006-05-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Formaldehyde dismutase
ID:	FDM_PSEPU
AC:	Q52078
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	25.663
Number of residues:	67
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.676	924.750

% Hydrophobic	% Polar
31.75	68.25
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	77.78 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
9.4242	70.6956	43.0289

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
C5N	SG	CYS- 45	3.8	0	Hydrophobic	false
O1N	N	GLY- 46	2.97	131.5	H-Bond (Protein Donor)	false
C2D	CB	SER- 47	4.31	0	Hydrophobic	false
O2D	OG	SER- 47	2.66	160.89	H-Bond (Ligand Donor)	false
O3D	NE2	HIS- 50	2.93	163.49	H-Bond (Protein Donor)	false
C5N	CG2	ILE- 170	4.5	0	Hydrophobic	false
C3N	CG2	THR- 173	3.66	0	Hydrophobic	false
O2N	N	VAL- 197	3.21	152.85	H-Bond (Protein Donor)	false
C5D	CB	VAL- 197	3.93	0	Hydrophobic	false
C5N	CG2	VAL- 197	4.27	0	Hydrophobic	false
O3B	OD2	ASP- 217	2.85	176.36	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 217	2.66	161.7	H-Bond (Ligand Donor)	false
N7A	NE2	GLN- 218	3.36	145.99	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 222	2.69	142.07	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 222	2.79	139.39	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 222	3.64	0	Ionic (Protein Cationic)	false
C1B	CG1	VAL- 262	4.4	0	Hydrophobic	false
O3D	O	VAL- 262	2.71	168.03	H-Bond (Ligand Donor)	false
N7A	N	HIS- 267	2.98	169.98	H-Bond (Protein Donor)	false
N6A	O	HIS- 267	2.81	138.63	H-Bond (Ligand Donor)	false
N7N	O	PRO- 298	2.55	151.6	H-Bond (Ligand Donor)	false
C2D	CG1	ILE- 300	4.16	0	Hydrophobic	false
C3N	CG1	ILE- 300	4.37	0	Hydrophobic	false
N7N	O	GLY- 335	3.31	137.68	H-Bond (Ligand Donor)	false
O7N	N	ALA- 337	2.89	175.09	H-Bond (Protein Donor)	false
O2N	O	HOH- 1411	2.68	167.67	H-Bond (Protein Donor)	false
O2A	O	HOH- 1427	2.69	156.67	H-Bond (Protein Donor)	false