scPDB - 1u08 entry

Protein Data Bank Entry:

PDB ID : 1u08

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2004-07-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine aminotransferase
ID:	YBDL_ECOLI
AC:	P77806
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
B	9 %

Ligand binding site composition:

B-Factor:	23.571
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.948	806.625

% Hydrophobic	% Polar
60.67	39.33
According to VolSite

Ligand :

HET Code:	PLP
Formula:	C8H8NO6P
Molecular weight:	245.126 g/mol
DrugBank ID:	DB00114
Buried Surface Area:	77.47 %
Polar Surface area:	132.42 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
13.0677	14.5541	18.0222

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
C4A	CZ	TYR- 63	4.25	0	Hydrophobic	false
O2P	OH	TYR- 63	2.67	164.36	H-Bond (Protein Donor)	false
C5A	CB	ALA- 100	4.2	0	Hydrophobic	false
O1P	N	ALA- 100	2.73	168.77	H-Bond (Protein Donor)	false
O3P	N	THR- 101	2.89	160.68	H-Bond (Protein Donor)	false
O3P	OG1	THR- 101	2.73	153.99	H-Bond (Protein Donor)	false
C2A	CG	TYR- 125	3.87	0	Hydrophobic	false
C4A	CZ	TYR- 125	3.86	0	Hydrophobic	false
C5A	CZ	TYR- 125	4.13	0	Hydrophobic	false
DuAr	DuAr	TYR- 125	3.61	0	Aromatic Face/Face	false
C2A	CB	ASN- 174	3.92	0	Hydrophobic	false
O3	ND2	ASN- 174	2.76	154.54	H-Bond (Protein Donor)	false
N1	OD1	ASP- 202	3.45	127.45	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 202	2.71	168.11	H-Bond (Ligand Donor)	false
C2A	CG2	VAL- 204	3.86	0	Hydrophobic	false
C5	CG1	VAL- 204	4.45	0	Hydrophobic	false
C3	CG2	VAL- 204	3.96	0	Hydrophobic	false
C2A	CE2	TYR- 205	3.95	0	Hydrophobic	false
O1P	OG	SER- 233	2.61	156.33	H-Bond (Protein Donor)	false
C4A	CD	LYS- 236	4.09	0	Hydrophobic	false
C4	CE	LYS- 236	3.75	0	Hydrophobic	false
O2P	NZ	LYS- 244	3.34	128.29	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 244	2.91	155.74	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 244	3.34	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 244	2.91	0	Ionic (Protein Cationic)	false