scPDB - 3rf7 entry

Protein Data Bank Entry:

PDB ID : 3rf7

Resolution :2.120 Å

Experimental Method : X-ray

Deposition Date : 2011-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Iron-containing alcohol dehydrogenase
ID:	Q12MB1_SHEDO
AC:	Q12MB1
Organism:	Shewanella denitrificans
Reign:	Bacteria
TaxID:	318161
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.718
Number of residues:	59
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	3
Water Molecules:	4
Cofactors:
Metals:	FE CA

Cavity properties

Ligandability	Volume (Å3)
0.726	688.500

% Hydrophobic	% Polar
43.63	56.37
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	68.41 %
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
68.9492	20.231	41.9026

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
O2B	OD2	ASP- 42	3.04	136.99	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 42	2.78	158.05	H-Bond (Ligand Donor)	false
C2B	CG1	VAL- 44	4.44	0	Hydrophobic	false
C3B	CG2	VAL- 67	3.94	0	Hydrophobic	false
C3D	CG	GLU- 70	4.13	0	Hydrophobic	false
O2N	N	GLY- 100	2.88	177.01	H-Bond (Protein Donor)	false
O1A	N	SER- 101	3.11	155.27	H-Bond (Protein Donor)	false
O2A	OG	SER- 101	2.8	172.46	H-Bond (Protein Donor)	false
O5D	N	SER- 101	3.49	122.08	H-Bond (Protein Donor)	false
C4D	CB	SER- 101	4.41	0	Hydrophobic	false
N7N	OD1	ASP- 104	2.75	121.26	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 104	3.07	162.34	H-Bond (Ligand Donor)	false
N7A	OG1	THR- 140	2.86	162.73	H-Bond (Protein Donor)	false
N6A	O	THR- 140	2.97	133.44	H-Bond (Ligand Donor)	false
C5D	CG2	THR- 144	3.96	0	Hydrophobic	false
C5N	CB	THR- 144	3.93	0	Hydrophobic	false
C3N	CB	ALA- 146	4.08	0	Hydrophobic	false
O7N	OG	SER- 149	2.53	157.93	H-Bond (Protein Donor)	false
N7N	OG	SER- 149	3.42	120.23	H-Bond (Ligand Donor)	false
N7N	O	THR- 151	2.93	149.16	H-Bond (Ligand Donor)	false
C3N	CG2	VAL- 153	4.1	0	Hydrophobic	false
C5B	CG	GLN- 187	3.99	0	Hydrophobic	false
O1N	OG1	THR- 191	3	175.13	H-Bond (Protein Donor)	false
C5D	CB	HIS- 272	4.32	0	Hydrophobic	false
C2D	CB	HIS- 272	3.74	0	Hydrophobic	false
O1A	O	HOH- 403	2.63	152.18	H-Bond (Protein Donor)	false
O2N	O	HOH- 706	2.71	179.98	H-Bond (Protein Donor)	false