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Table 1 Analyzed protein dataset.

From: Computational prediction of hinge axes in proteins

Protein

PDB ID

KINARI cutoff

Pinned cluster

Moving cluster

Twist purity

Calmodulin (calcium-free)

1CFD

default

0

1

77.1269

Calmodulin (Ca 2+ -bound; open)

1CLL

-2

0

1

95.435

Calmodulin (Ca2+ -bound; closed)

2BBM(A)

default

4

7

150.339

LAO binding protein (open)

1LST

default

0

1

91.5669

LAO binding protein (closed)

2LAO

default

0

1

98.1407

Bence-Jones protein (open)

4BJL(B)

-1.25

0

1

97.0153

Bence-Jones protein (closed)

4BJL(A)

-1.25

0

1

99.0822

cAMP-dependent protein kinase (open)

1CTP

-1.9

0

2

89.7223

cAMP-dependent protein kinase (closed)

1ATP

-1.9

0

1

93.2537

Adenylate kinase (open)

2AK3(A)

default

0

1

95.2801

Adenylate kinase (closed)

1AKE(A)

-2.5

1

0

91.4916

Glutamine binding protein (open)

1GGG(A)

default

1

0

105.321

Glutamine binding protein (closed)

1WDN

-2

0

1

90

DNA polymerase β (open)

2BPG(A)

default

0

1

109.657

DNA polymerase β (closed)

1BPD

default

0

1

86.6385

Inorganic pyrophosphatase (open)

1K23(A)

default

0

1

91.6584

Inorganic pyrophosphatase (closed)

1K20(A)

-3

1

0

80.6779

Ribose binding protein (open)

1URP(C)

-2

0

1

75.4811

Ribose binding protein (closed)

2DRI

-2.65

1

0

89.4672

  1. For structures where the PDB contains more than one chain, the analyzed chain is indicated within parentheses. The KINARI cutoff column lists the value of the energy cutoff used for including hydrogen bonds. Bold entries indicate structures for which predicted axis of motion is consistent with second conformation.