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. 2024 May 7;128(19):4602–4620. doi: 10.1021/acs.jpcb.3c08469

Table 1. List of the 39 Protein Structures Solved by X-ray Diffraction Used in This Studya.

PDB ID protein name organism NR 310 (%)b α (%)b β (%)b pH res. [Å] Rwork Rfree force field
4LFQ potassium channel toxin L-ShK Stichodactyla helianthus 35 9 34 7.0 1.1 0.13 0.16 all
2NLS human β-defensin-1, mutant Q24A Homo sapiens 36 19 31 7.5 1.0 0.11 0.12 54A7/8
3E7U plectasin Pseudoplectania nigrella 40 3 23 25 7.5 1.4 0.16 0.18 all
2GKT turkey ovomucoid third domain Meleagris gallopavo 51 20 16 7.5 1.2 0.13 0.15 all
3CA7 protein Spitz Drosophila melanogaster 52 12 38 6.5 1.5 0.2 0.24 54A7/8
1PGBc protein G, B1 domain Streptococcus sp. gx7805 56 25 43 4.5 1.9 0.20 all
1ZLM osteoclast stimulating factor 1 Homo sapiens 58 5 48 7.5 1.1 0.16 0.21 all
1SHGc α-spectrin Gallus gallus 62 5 49 4.0 1.8 0.2 0.28 all
1UCS antifreeze peptide RD1 Lycodichthys dearborni 64 14 6 25 7.5 0.6 0.14 0.15 all
1ZVG α-like neurotoxin BmK-I Mesobuthus martensii 66 2 15 30 6.0 1.2 0.16 0.16 all
1YU5c villin headpiece Gallus gallus 67 10 45 7.0 1.4 0.19 0.22 all
1MJC major cold shock protein Escherichia coli 69 4 46 7.5 2.0 0.19 all
1UBIc ubiquitin Homo sapiens 76 8 16 33 5.6 1.8 0.17 all
2J8B human CD59 glycoprotein Homo sapiens 79 8 10 32 7.5 1.1 0.17 0.2 54A7/8
2PNEd glycine-rich antifreeze protein Hypogastrura harveyi 81 6.5 1.0 0.14 0.16 all
1ULRe putative acylphosphatase Thermus thermophilus 88 1 28 38 7.0 1.3 0.19 0.22 all
1A19c barstar, mutant C82A Bacillus amyloliquefaciens 90 2 44 17 6.5 2.8 0.2 0.29 54A7/8
4RWU protein Sis1 Saccharomyces cerevisiae s288c 92 62 7.0 1.2 0.12 0.15 54A7/8
1T2I ribonuclease Sa Streptomyces aureofaciens 96 3 11 22 7.2 1.1 0.13 0.17 all
2YXF β-2-microglobulin Homo sapiens 100 49 7.0 1.1 0.18 0.2 54A7/8
2CWRc chitin binding domain of chitinase Pyrococcus furiosus 103 62 6.5 1.7 0.19 0.23 all
2RB8 tenascin Homo sapiens 104 48 7.5 1.4 0.17 0.2 54A7/8
1EW4 CyaY Escherichia coli 106 31 32 5.1 1.4 0.19 0.21 all
2PPO FK506 binding protein-12 (FKBP12), mutant E60A Homo sapiens 107 4 7 37 7.0 1.3 0.13 0.18 all
2PND Murine CRIg Mus musculus 119 5 51 7.5 1.0 0.12 0.14 54A7/8
1FAZc phospholipase A2 Streptomyces violaceoruber 122 10 57 6.0 1.4 0.19 0.23 all
1TVQc chicken liver basic fatty acid binding protein Gallus gallus 125 11 58 7.5 2.0 0.23 0.27 all
1AKIc lysozyme Gallus gallus 129 13 30 11 4.5 1.5 0.21 all
1UXZ cellulase B Cellvibrio mixtus 131 2 56 7.0 1.4 0.16 0.18 all
1QK8 tryparedoxin-I Crithidia fasciculata 146 8 27 22 7.5 1.4 0.19 0.22 all
1NG6 hypothetical protein yqeY Bacillus subtilis 148 4 74 5.5 1.4 0.21 0.25 all
2WLW TRIM5-CypA Macaca mulatta 165 3 12 32 7.4 1.5 0.16 0.19 54A7/8
3EYE PTS system N-acetylgalactosamine-specific IIB component 1 Escherichia coli o157:h7 168 5 35 24 7.0 1.4 0.19 0.22 54A7/8
1FL0 endothelial monocyte-activating polypeptide II Homo sapiens 171 7 2 37 7.5 1.5 0.22 0.22 all
1AMM γ-crystallin B Bos taurus 174 6 3 40 6.8 1.2 0.18 all
1TUAe hypothetical protein APE0754 Aeropyrum pernix 191 7 53 18 7.0 1.5 0.21 0.23 all
2PTH peptidyl-tRNA hydrolase Escherichia coli 193 7 38 21 7.5 1.2 0.2 0.21 54A7/8
3WP5 xylanase CDBFV, mutant E109A Neocallimastix patriciarum 227 2 8 54 6.5 1.3 0.15 0.18 all
4MHP putative glutaminyl cyclase Ixodes scapularis 326 6 33 17 7.5 1.1 0.17 0.19 all
a

Abbreviations: NR = number of residues; 310 = 310-helix; α = α-helix; β = β-strand + β-bridge.

b

Secondary structure percentages as assigned by DSSP.

c

Has a paired NMR structure.

d

Polyproline II spiral only, not detected by DSSP.

e

pH not reported, set to 7.0.