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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 (Å) Start End RMSD (Å) 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.