6RHL

Room temperature data of Galectin-3C in complex with a pair of enantiomeric ligands: R enantiomer

6RHL の概要

• エントリーDOI: 10.2210/pdb6rhl/pdb
• 分子名称: Galectin-3, (2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-2-[(2~{R})-3-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-2-oxidanyl-propyl]sulfanyl-6-(hydroxymethyl)oxane-3,5-diol (3 entities in total)
• 機能のキーワード: lectin, carbohydrate-binding protein, galactose-specific lectin 3, galactoside-binding protein, galbp, ige-6 binding protein, l-31, laminin-binding protein, lectin l-29, mac-2, sugar binding protein
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16261.62

構造登録者

Kumar, R.,Verteramo, M.L.,Nilsson, U.J.,Logan, D.T. (登録日: 2019-04-22, 公開日: 2019-08-21, 最終更新日: 2024-01-24)

主引用文献

Caldararu, O.,Kumar, R.,Oksanen, E.,Logan, D.T.,Ryde, U.
Are crystallographic B-factors suitable for calculating protein conformational entropy?
Phys Chem Chem Phys, 21:18149-18160, 2019

PubMed Abstract: Conformational entropies are of great interest when studying the binding of small ligands to proteins or the interaction of proteins. Unfortunately, there are no experimental methods available to measure conformational entropies of all groups in a protein. Instead, they are normally estimated from molecular dynamics (MD) simulations, although such methods show problems with convergence and correlation of motions, and depend on the accuracy of the underlying potential-energy function. Crystallographic atomic displacement parameters (also known as B-factors) are available in all crystal structures and contain information about the atomic fluctuations, which can be converted to entropies. We have studied whether B-factors can be employed to extract conformational entropies for proteins by comparing such entropies to those measured by NMR relaxation experiments or obtained from MD simulations in solution or in the crystal. Unfortunately, our results show that B-factor entropies are unreliable, because they include the movement and rotation of the entire protein, they exclude correlation of the movements and they include contributions other than the fluctuations, e.g. static disorder, as well as errors in the model and the scattering factors. We have tried to reduce the first problem by employing translation-libration-screw refinement, the second by employing a description of the correlated movement from MD simulations, and the third by studying only the change in entropy when a pair of ligands binds to the same protein, thoroughly re-refining the structures in exactly the same way and using the same set of alternative conformations. However, the experimental B-factors seem to be incompatible with fluctuations from MD simulations and the precision is too poor to give any reliable entropies.

PubMed: 31389436
DOI: 10.1039/c9cp02504a

実験手法

X-RAY DIFFRACTION (1.299 Å)