scPDB - 1kbi entry

Protein Data Bank Entry:

PDB ID : 1kbi

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2001-11-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome b2, mitochondrial
ID:	CYB2_YEAST
AC:	P00175
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.1.2.3

Chains:

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

Ligand binding site composition:

B-Factor:	22.255
Number of residues:	47
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.207	408.375

% Hydrophobic	% Polar
36.36	63.64
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	85.59 %
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
66.0181	56.4146	0.041

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
C7M	CE1	TYR- 143	3.63	0	Hydrophobic	false
C7M	CD2	TYR- 144	3.53	0	Hydrophobic	false
O2'	OG	SER- 195	2.67	152.18	H-Bond (Protein Donor)	false
C3'	CB	SER- 195	4.1	0	Hydrophobic	false
O2'	O	ALA- 196	2.56	162.35	H-Bond (Ligand Donor)	false
C6	CB	THR- 197	3.72	0	Hydrophobic	false
C9	CG2	THR- 197	3.9	0	Hydrophobic	false
N5	N	ALA- 198	3.15	151.07	H-Bond (Protein Donor)	false
O4	OG	SER- 228	2.73	133.33	H-Bond (Protein Donor)	false
N3	OE1	GLN- 252	3.02	140.8	H-Bond (Ligand Donor)	false
O2	OG1	THR- 280	2.69	156.49	H-Bond (Protein Donor)	false
N1	NZ	LYS- 349	2.95	121.16	H-Bond (Protein Donor)	false
O2	NZ	LYS- 349	2.76	139.59	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 349	3.07	153.55	H-Bond (Protein Donor)	false
C9	CD	ARG- 376	3.56	0	Hydrophobic	false
O3'	OD2	ASP- 409	2.74	152.6	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 409	4.01	0	Hydrophobic	false
O3P	N	GLY- 411	2.92	172.63	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 413	3.32	158.13	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 413	2.68	162.92	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 413	3.46	126.52	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 413	3.5	0	Ionic (Protein Cationic)	false
O2P	N	GLY- 432	2.9	162.99	H-Bond (Protein Donor)	false
C8M	CG	ARG- 433	3.39	0	Hydrophobic	false
O1P	CZ	ARG- 433	3.82	0	Ionic (Protein Cationic)	false
O1P	N	ARG- 433	3	173.7	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 433	3.24	120.82	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 436	3.55	0	Hydrophobic	false
O2P	O	HOH- 771	2.8	179.97	H-Bond (Protein Donor)	false
O3P	O	HOH- 814	2.84	179.99	H-Bond (Protein Donor)	false