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Table 1 20 apo-holo pairs of calcium-binding proteins for validation

From: Prediction of calcium-binding sites by combining loop-modeling with machine learning

  

Holo structure

Apo structure

 

Loop

Protein and calcium ID

Protein name

PDB ID

Chain ID

PDB ID

Chain ID

All RMSD (Ã…)

Start

End

RMSD (Ã…)

Sequence

1B9AA110

PARVALBUMIN

1B9A

A

1B8C

A

1.48

51

62

2.68

AQDKSGFIEEDE

1C1R_247

CHYMOTRYPSIN INHIBITOR 2

1C1R

A

1AZ8

A

0.60

70

80

0.13

EDNINVVE GNE

1DPO_246

TRYPSIN

1DPO

A

1BRB

E

0.73

70

80

0.37

E HNINVLE GNE

1DVIB275

CALPAIN

1DVI

B

1AJ5

B

2.06

111

121

2.36

AGDD ME VSATE

1DVIB277

CALPAIN

1DVI

B

1AJ5

A

1.75

184

195

0.90

D TD RSGTIGSNE

1F6SB202

ALPHA-LACTALBUMIN

1F6S

B

1F6R

C

0.86

79

89

0.33

KFLDDD LTDD I

1HAZB1246

BETA-CASOMORPHIN-7

1HAZ

B

1FLE

E

1.06

70

80

0.23

E HNLNQNNGTE

1I40_305

INORGANIC PYROPHOSPHATASE

1I40

A

1MJW

A

0.55

138

146

0.25

FE HYKD LE K

1K94_998

GRANCALCIN

1K94

A

1F4Q

B

1.23

130

143

0.68

TVDQDGSGTVE HHE

1K94_999

GRANCALCIN

1K94

A

1F4Q

A

1.35

62

72

0.67

AGQDGE VD AEE

1K96A91

S100A6

1K96

A

1K8U

A

4.15

24

34

1.45

GD KHTLSKKE L

1KXQB4003

ALPHA-AMYLASE, PANCREATIC

1KXQ

B

1KXV

A

0.46

165

172

0.17

LLD LALE K

1NLS_240

CONCANAVALIN A

1NLS

A

1DQ0

A

0.31

9

20

0.47

LD TYPNTD IGD P

1NOL_632

HEMOCYANIN (SUBUNIT TYPE II)

1NOL

A

1OXY

A

0.55

577

584

0.13

VD AVSYCG

1PSH_1

PHOSPHOLIPASE A2

1PSH

A

1A3D

A

0.61

25

34

1.41

GCYCGRGGSG

1QMDA403

PHOSPHOLIPASE C

1QMD

A

1QM6

A

0.20

265

270

0.13

SGE KD A

1QMDA405

PHOSPHOLIPASE C

1QMD

A

1QM6

A

0.20

292

299

0.14

MD NPGND F

2POR_304

PORIN

2POR

A

3POR

A

1.00

135

145

0.98

SD GKVGE TSED

3LHM_131

HUMAN LYSOZYME

3LHM

A

2LHM

A

0.21

83

94

0.40

ALLDD NIADD VA

5CHY_401

CHEY

5CHY

A

3CHY

A

0.35

55

63

0.15

ISD WNMPNM

  1. PDB ID (PDB code followed by chain identifier and calcium index) and protein names are from PDB (column 1-2). PDB ID and chain ID are from PDB (column 3-6). The RMSD between the apo and the holo structures is given in column 7. Columns 8, 9 and 11 list the information of calcium-binding loops, including the loop starting and ending residue numbers, and the loop sequence. The RMSD between calcium-binding loops in the apo and the holo structures is given in column 10.