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Table 2 Consensus information about each pattern

From: Automatic generation of 3D motifs for classification of protein binding sites

Pattern

Rep.

Ligand

Size

Atoms

Function

EC

CATH

DALI

IPR

PS

ADP0

1vom

ADP

6

11

Myosin

/

1.10.162.10

1.10.183.10

1.10.465.10

3.30.538.10

1237

001093

001609

 

ADP1

1q0b

ADP

7

7

Kinesin

/

3.40.850.10

1236

001752

50067

00411

ADP2

1b62

ADP

10

8

  

3.30.565.10

(846, 847, 848)

003594

 

ADP3

1qf9

ADP

8

23

Transferase

2.7. (2.7.1., 2.7.4.)

3.40.50.300

   

ADP4

1ehi

ADP

5

18

Ligase (60%) Transferase (40%)

 

3.30.

   

ADP5

1njf

ADP

4

17

  

1.10.8.60

3.40.50.300

1062

003593

 

ADP6

1oxu

ADP

5

6

Abc transporter

/

3.40.50.300

1069

1071

003593

003439

00211

50893

AMP0

1v26

AMP

4

27

Ligase

 

2.30.38.10

3.30.300.30

3.40.50.980

736

992

000873

00455

ATP0

1y8q

ATP

3

71

Ligase

ND

3.40.50.70

851

000205

000594

 

AxP0

2a40

ADP

ATP

13

42

Actin (85%) Heat shock (15%)

/

3.30.420.40

3.90.640.10

1175

  

AxP1

1j1c

ADP

ATP

20

45

Kinase

2.7.1.

1.10.510.10

3.30.200.20

593

000719

50011

AxP2

1ses

AMP

ATP

8

51

Ligase

6.1.1.

3.30.930.10

1116

 

50862

AxP3

1o97

AMP

ATP

7

42

  

3.40.50.620

(973 974 975)

  
  1. This table consists of the name of the pattern, its PDB representative (Rep.), names of ligands the pattern was created from, the size of the cluster, the number of atoms in the pattern, the annotated function, the EC (Enzyme Commission) number if relevant [35], the protein fold classifications according to CATH [3] and DALI [2], and finally detected sequence motifs according to InterPro (IPR) [11] and PROSITE (PS) [10]. When consensus values could not be found, but close alternatives were available, values are shown between brackets. Finally, when data was not available through PDBSum, it was inferred when possible using homologues; in this case values are shown in italic. Otherwise when not enough data was available to generate a meaningful consensus value, the code 'ND' is used.