scPDB - 3bnk entry

Protein Data Bank Entry:

PDB ID : 3bnk

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2007-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavoredoxin
ID:	Q8TTU7_METAC
AC:	Q8TTU7
Organism:	Methanosarcina acetivorans
Reign:	Archaea
TaxID:	188937
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	20.160
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.000	567.000

% Hydrophobic	% Polar
45.24	54.76
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	75.71 %
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
6.13555	-9.42868	16.52

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
O3P	ND2	ASN- 30	2.87	170.3	H-Bond (Protein Donor)	false
C2'	CE	MET- 32	4.15	0	Hydrophobic	false
C5'	CB	MET- 32	3.67	0	Hydrophobic	false
O2'	O	ALA- 33	2.85	153.4	H-Bond (Ligand Donor)	false
C8	CB	ALA- 33	3.66	0	Hydrophobic	false
O4	N	GLY- 35	3.03	152.59	H-Bond (Protein Donor)	false
N5	N	GLY- 35	3.19	132.48	H-Bond (Protein Donor)	false
O4	N	TRP- 36	2.97	157.62	H-Bond (Protein Donor)	false
N3	O	GLY- 50	2.74	151.49	H-Bond (Ligand Donor)	false
O2	N	ASN- 52	2.73	174.68	H-Bond (Protein Donor)	false
N1	NE2	HIS- 55	3.1	133.69	H-Bond (Protein Donor)	false
C5'	CB	HIS- 55	4.11	0	Hydrophobic	false
O1P	N	TYR- 56	3.07	166.97	H-Bond (Protein Donor)	false
O2P	N	TYR- 56	3.29	123.22	H-Bond (Protein Donor)	false
O2P	N	THR- 57	2.92	139.41	H-Bond (Protein Donor)	false
O4'	O	VAL- 86	2.74	134.77	H-Bond (Ligand Donor)	false
O1P	OG	SER- 87	2.63	154.2	H-Bond (Protein Donor)	false
O3P	N	GLY- 88	2.72	162.63	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 93	2.73	171.22	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 93	2.73	0	Ionic (Protein Cationic)	false
C7M	CD2	LEU- 162	3.54	0	Hydrophobic	false
C8	CE	MET- 164	4.08	0	Hydrophobic	false
C7M	CE2	TYR- 169	3.75	0	Hydrophobic	false
C8M	CD2	LEU- 180	3.62	0	Hydrophobic	false