scPDB - 3rup entry

Protein Data Bank Entry:

PDB ID : 3rup

Resolution :1.990 Å

Experimental Method : X-ray

Deposition Date : 2011-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biotin carboxylase
ID:	ACCC_ECOLI
AC:	P24182
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.3.4.14

Chains:

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

Ligand binding site composition:

B-Factor:	16.636
Number of residues:	40
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:	ADP
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
1.115	1329.750

% Hydrophobic	% Polar
34.01	65.99
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	62.16 %
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
63.9623	1.89881	13.3891

Binding mode :

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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
C5'	CD1	TYR- 82	3.73	0	Hydrophobic	false
O1A	N	GLY- 165	3.49	123.86	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 237	2.94	160.38	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 238	2.93	153.32	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 238	2.93	0	Ionic (Protein Cationic)	false
O1B	ND2	ASN- 290	2.94	123.41	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 292	3.65	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 292	3.59	0	Ionic (Protein Cationic)	false
O1B	NH2	ARG- 292	2.76	157.43	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 292	2.72	177.53	H-Bond (Protein Donor)	false
O2B	N	VAL- 295	2.85	172.05	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 295	3.45	0	Hydrophobic	false
O3B	OE2	GLU- 296	2.58	156.29	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 338	3.23	120.78	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 338	2.7	175.09	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 338	3.49	127.71	H-Bond (Protein Donor)	false
O3A	NH2	ARG- 338	3.29	153.02	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 338	3.53	0	Ionic (Protein Cationic)	false
O3'	OD2	ASP- 382	2.63	123.4	H-Bond (Ligand Donor)	false