Kamphuis I G, Kalk K H, Swarte M B, Drenth J
J Mol Biol. 1984 Oct 25;179(2):233-56. doi: 10.1016/0022-2836(84)90467-4.
Papain is a sulfhydryl protease from the latex of the papaya fruit. Its molecules consist of one polypeptide chain with 212 amino acid residues. The chain is folded into two domains with the active site in a groove between the domains. We have refined the crystal structure of papain, in which the sulfhydryl group was oxidized, by a restrained least-squares procedure at 1.65 A to an R-factor of 16.1%. The estimated accuracy in the atomic co-ordinates is 0.1 A, except for disordered atoms. All phi/psi angles for non-glycine residues are found within the outer limit boundary of a Ramachandran plot and this provides another check on the quality of the model. In the alpha-helical parts of the structure, the C = O bonds are directed more away from the helix axis than in a classical alpha-helix, leading to somewhat longer hydrogen bonds, 2.98 A, compared to 2.89 A. The hydrogen-bonding parameters and conformational angles in the anti-parallel beta-sheet structure show a large diversity. Hydrogen bonds in the core of the sheet are generally shorter than those at the more twisted ends. The average value is 2.91 A. The hydrogen bond distance Ni+3-Oi in turns is relatively long and the geometry is far from linear. Hydrogen bond formation, therefore, is perhaps not an essential prerequisite for turn formation. Although the crystallization medium is 62% (w/w) methanol in water, only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules. The water molecules play an important role in maintaining structural stability. This is specially true for internal water. Twenty-one water molecules are located in contact areas between adjacent papain molecules. It seems as if the enzyme is trapped in a grid of water molecules with only a limited number of direct interactions between the protein molecules. The residues in the active site cleft belong to the most static parts of the structure. In general, disorder in atomic positions increases when going from the interior of the protein molecule to its surface. This behavior was quantified and it was found that the point of minimum disorder is near the molecular centroid.
木瓜蛋白酶是一种源自番木瓜果实乳汁的巯基蛋白酶。它的分子由一条含有212个氨基酸残基的多肽链组成。该链折叠成两个结构域，活性位点位于两个结构域之间的凹槽中。我们通过约束最小二乘法将巯基被氧化的木瓜蛋白酶晶体结构精修至1.65埃，R因子为16.1%。除了无序原子外，原子坐标的估计精度为0.1埃。非甘氨酸残基的所有φ/ψ角均在拉氏图的外限边界内，这为模型质量提供了另一项检验。在结构的α螺旋部分，C=O键比经典α螺旋中更远离螺旋轴，导致氢键稍长，为2.98埃，而经典α螺旋中为2.89埃。反平行β折叠结构中的氢键参数和构象角表现出很大的多样性。折叠片层核心中的氢键通常比扭曲程度更大的末端处的氢键短。平均值为2.91埃。转角处的氢键距离Ni+3-Oi相对较长，且几何形状远非线性。因此，氢键形成可能不是转角形成的必要先决条件。尽管结晶介质是62%（w/w）甲醇水溶液，但在224个溶剂分子中，只有29个可以确定地被视为甲醇分子。水分子在维持结构稳定性方面起着重要作用。内部水分子尤其如此。21个水分子位于相邻木瓜蛋白酶分子之间的接触区域。似乎酶被困在水分子网格中，蛋白质分子之间只有有限数量的直接相互作用。活性位点裂隙中的残基属于结构中最稳定的部分。一般来说，从蛋白质分子内部到其表面，原子位置的无序性增加。这种行为被量化，发现无序性最小的点靠近分子质心。
