Table 2 Structures of enzyme/inhibitor-complexes.
From: Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections
PDB ID | 7Z3T | 7QKC | 7Z58 | 7QKB | 7Z3U | 7QKA | 7QGW | 8C3D |
|---|---|---|---|---|---|---|---|---|
Protein/Compound | CatL | CatL/S-Calp | CatL/Calpeptin | CatL/GC-376 | Mpro/S-Calp | Mpro/GC-376 | CatV/Calp | CatK/S-Calp |
Data collection | ||||||||
Space group | P1 | P1 | P1 | P1 | P 21 21 21 | C 1 2 1 | P43 21 2 | C1 2 1 |
Cell dimensions | ||||||||
a, b, c (Å) | 56.94, 62.14, 67.47 | 57.05, 62.46, 67.54 | 57.18, 62.45, 67.82 | 57.29, 62.45, 67.82 | 67.692, 99.598, 103.261 | 113.675, 53.356, 44.994 | 94.24, 94.24, 126.96 | 94.63, 41.62, 65.66 |
α, β, γ (°) | 105.166, 94.226, 115.576 | 105.32, 93.91, 115.39 | 105.578, 93.134, 115.562 | 105.306, 93.523, 115.929 | 90, 90, 90 | 90, 102.511, 90 | 90, 90, 90 | 90, 121.01, 90.0 |
Resolution (Å)a | 49.94 - 1.6 (1.657 - 1.6) | 44.27 – 1.69 (1.752 - 1.691) | 49.64 - 1.35 (1.398 - 1.35) | 44.25 - 1.8 (1.864 - 1.8) | 49.22 - 1.72 (1.782 - 1.72) | 48.09 - 1.8 (1.864 - 1.8) | 47.12 - 1.3 (1.35 - 1.303) | 34.94 - 2.0 (2.12 – 2.00) |
Rmergea | 0.1661 (2.183) | 0.1705 (1.244) | 0.2549 (1.335) | 0.1346 (0.9518) | 0.101 (2.172) | 0.04322 (0.53) | 0.0548 (1.023) | 0.100 (0.232) |
Rmeasa | 0.1793 (2.345) | 0.1809 (1.378) | 0.2568 (1.364) | 0.1476 (1.115) | 0.1086 (2.328) | 0.04674 (0.5756) | 0.05597 (1.057) | 0.110 (0.270) |
Rpima | 0.06553 (0.839) | 0.05976 (0.579) | 0.03067 (0.2767) | 0.05975 (0.5693) | 0.03923 (0.8283) | 0.01761 (0.2213) | 0.0113 (0.2616) | 0.0449 (0.1304) |
Mean I/sigma (I)a | 9.07 (2.33) | 9.33 (1.57) | 16.83 (2.11) | 9.62 (1.99) | 12.54 (0.95) | 23.40 (3.05) | 32.94 (2.56) | 23.32 (11.35) |
CC 1/2a | 0.99 (0.55) | 0.996 (0.567) | 0.999 (0.835) | 0.994 (0.73) | 0.999 (0.524) | 1 (0.9) | 1 (0.837) | 0.997 (0.961) |
Completeness (%)a | 97.22 (96.66) | 98.06 (83.93) | 99.98 (99.90) | 90.98 (81.98) | 99.70 (98.31) | 98.89 (98.22) | 99.91 (99.16) | 98.9 (96.2) |
Redundancya | 7.2 (7.6) | 8.7 (5.2) | 61.1 (23.1) | 5.0 (3.3) | 7.5 (7.7) | 6.9 (6.6) | 23.7 (16.0) | 5.89 (4.45) |
Refinement | ||||||||
Resolution (Å) | 49.94 - 1.6 (1.657 - 1.6) | 44.27 - 1.691 (1.752 - 1.691) | 49.64 - 1.35 (1.398 - 1.35) | 44.25 - 1.8 (1.864 - 1.8) | 49.22 - 1.72 (1.782 - 1.72) | 48.09 - 1.8 (1.864 - 1.8) | 47.12 - 1.303 (1.35 - 1.303) | 34.94 - 2.0 (2.03 – 2.00) |
No. reflectionsa | 100909 (10010) | 87087 (7453) | 175655 (17545) | 67329 (6065) | 74542 (7273) | 24243 (2368) | 139006 (13653) | 14932 (682) |
Rworka/Rfree | 0.1547 (0.2424)/0.1760 (0.2612) | 0.1465 (0.2700)/0.1790 (0.3048) | 0.1300 (0.2262)/0.1574 (0.2515) | 0.1694 (0.3041)/0.2030 (0.3546) | 0.1865 (0.3802)/ 0.2157 (0.3986) | 0.1629 (0.2237)/0.2072 (0.3017) | 0.1718 (0.2454) / 0.1956(0.2775)b | 0.1959 (0.2268) / 0.2405 (0.1887)b |
No. non-hydrogen atoms | 7801 | 7645 | 8359 | 7279 | 5442 | 2711 | 1913 | |
Protein | 7057 | 6822 | 7161 | 6785 | 4911 | 2417 | 3479 | 1649 |
Ligand/ion | 140 | 153 | 230 | 222 | 94 | 70 | 196 | 26 |
Water | 586 | 670 | 968 | 272 | 437 | 224 | 2040 | 238 |
B-factors | 29.23 | 27.28 | 20.09 | 52.57 | 41.32 | 36.95 | 25.89 | 11.37 |
Protein | 28.5 | 26.1 | 18.17 | 52.2 | 40.85 | 36.95 | 19.42 | 9.42 |
Ligand/ion | 48.56 | 50.48 | 38.12 | 65.86 | 53.36 | 40.68 | 56.23 | 19.49 |
Water | 33.44 | 34 | 29.99 | 51.17 | 44.02 | 39.66 | 53.05 | 24.96 |
R.m.s. deviations | ||||||||
Bond lengths (Å) | 0.005 | 0.009 | 0.011 | 0.006 | 0.006 | 0.013 | 0.017 | 0.018 |
Bond angles (°) | 0.88 | 1.26 | 1.08 | 0.65 | 0.92 | 1.08 | 1.83 | 2.05 |
Ramachandran | ||||||||
favored | 97.78 | 97.56 | 97.58 | 96.84 | 98.1 | 98.02 | 97.26 | 96.7 |
allowed | 2.22 | 2.44 | 2.42 | 3.16 | 1.9 | 1.98 | 2.74 | 3.3 |
outliers | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
