Table 1.
20 apo-holo pairs of calcium-binding proteins for validation
| 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 | EDNINVVEGNE |
| 1DPO_246 | TRYPSIN | 1DPO | A | 1BRB | E | 0.73 | 70 | 80 | 0.37 | EHNINVLEGNE |
| 1DVIB275 | CALPAIN | 1DVI | B | 1AJ5 | B | 2.06 | 111 | 121 | 2.36 | AGDDMEVSATE |
| 1DVIB277 | CALPAIN | 1DVI | B | 1AJ5 | A | 1.75 | 184 | 195 | 0.90 | DTDRSGTIGSNE |
| 1F6SB202 | ALPHA-LACTALBUMIN | 1F6S | B | 1F6R | C | 0.86 | 79 | 89 | 0.33 | KFLDDDLTDDI |
| 1HAZB1246 | BETA-CASOMORPHIN-7 | 1HAZ | B | 1FLE | E | 1.06 | 70 | 80 | 0.23 | EHNLNQNNGTE |
| 1I40_305 | INORGANIC PYROPHOSPHATASE | 1I40 | A | 1MJW | A | 0.55 | 138 | 146 | 0.25 | FEHYKDLEK |
| 1K94_998 | GRANCALCIN | 1K94 | A | 1F4Q | B | 1.23 | 130 | 143 | 0.68 | TVDQDGSGTVEHHE |
| 1K94_999 | GRANCALCIN | 1K94 | A | 1F4Q | A | 1.35 | 62 | 72 | 0.67 | AGQDGEVDAEE |
| 1K96A91 | S100A6 | 1K96 | A | 1K8U | A | 4.15 | 24 | 34 | 1.45 | GDKHTLSKKEL |
| 1KXQB4003 | ALPHA-AMYLASE, PANCREATIC | 1KXQ | B | 1KXV | A | 0.46 | 165 | 172 | 0.17 | LLDLALEK |
| 1NLS_240 | CONCANAVALIN A | 1NLS | A | 1DQ0 | A | 0.31 | 9 | 20 | 0.47 | LDTYPNTDIGDP |
| 1NOL_632 | HEMOCYANIN (SUBUNIT TYPE II) | 1NOL | A | 1OXY | A | 0.55 | 577 | 584 | 0.13 | VDAVSYCG |
| 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 | SGEKDA |
| 1QMDA405 | PHOSPHOLIPASE C | 1QMD | A | 1QM6 | A | 0.20 | 292 | 299 | 0.14 | MDNPGNDF |
| 2POR_304 | PORIN | 2POR | A | 3POR | A | 1.00 | 135 | 145 | 0.98 | SDGKVGETSED |
| 3LHM_131 | HUMAN LYSOZYME | 3LHM | A | 2LHM | A | 0.21 | 83 | 94 | 0.40 | ALLDDNIADDVA |
| 5CHY_401 | CHEY | 5CHY | A | 3CHY | A | 0.35 | 55 | 63 | 0.15 | ISDWNMPNM |
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.