scPDB - 2ykv entry

Protein Data Bank Entry:

PDB ID : 2ykv

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-05-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-transaminase
ID:	A3EYF7_9RHIZ
AC:	A3EYF7
Organism:	Mesorhizobium sp. LUK
Reign:	Bacteria
TaxID:	398267
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	21 %
B	79 %

Ligand binding site composition:

B-Factor:	16.031
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.082	1218.375

% Hydrophobic	% Polar
39.06	60.94
According to VolSite

Ligand :

HET Code:	IK2
Formula:	C10H12N2O8P
Molecular weight:	319.185 g/mol
DrugBank ID:	DB02783
Buried Surface Area:	75.93 %
Polar Surface area:	176.73 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
36.3578	81.6532	23.0568

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
O1'	CZ	ARG- 54	3.68	0	Ionic (Protein Cationic)	false
O2'	CZ	ARG- 54	3.73	0	Ionic (Protein Cationic)	false
O1'	NE	ARG- 54	2.81	163.83	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 54	2.94	167.58	H-Bond (Protein Donor)	false
O3P	N	GLY- 145	3.02	155.32	H-Bond (Protein Donor)	false
O1P	N	THR- 146	2.87	147.55	H-Bond (Protein Donor)	false
O1P	OG1	THR- 146	2.58	156.13	H-Bond (Protein Donor)	false
C4A	CE2	TYR- 172	3.77	0	Hydrophobic	false
C1'	CE2	TYR- 172	4.28	0	Hydrophobic	false
C5A	CE2	TYR- 172	4.2	0	Hydrophobic	false
C2A	CG	GLU- 220	3.71	0	Hydrophobic	false
N1	OD1	ASP- 253	3.27	130.75	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 253	2.79	164.92	H-Bond (Ligand Donor)	false
C2A	CB	VAL- 255	4.15	0	Hydrophobic	false
C5	CG1	VAL- 255	3.82	0	Hydrophobic	false
OX	NZ	LYS- 280	3.02	166.99	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 280	3.34	0	Ionic (Protein Cationic)	false
C1'	CB	ALA- 312	3.78	0	Hydrophobic	false
O1'	N	GLY- 313	2.83	160.18	H-Bond (Protein Donor)	false
O2P	OG1	THR- 314	2.9	175.97	H-Bond (Protein Donor)	false
O2P	N	THR- 314	2.82	163.12	H-Bond (Protein Donor)	false
O3P	O	HOH- 2057	2.64	157.85	H-Bond (Protein Donor)	false