3G4V

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropentane bound to the XE4 cavity

3G4V の概要

• エントリーDOI: 10.2210/pdb3g4v/pdb
• 関連するPDBエントリー: 3G46 3G4R 3G4U 3G4W 3G4Y 3G52 3G53 3g4Q 3sdh 4sdh
• 分子名称: GLOBIN-1, PROTOPORPHYRIN IX CONTAINING FE, CARBON MONOXIDE, ... (5 entities in total)
• 機能のキーワード: oxygen transport, allostery, oxygen affinity, cytoplasm, heme, iron, metal-binding, oxygen storage/transport, oxygen binding
• 由来する生物種: Scapharca inaequivalvis (ARK CLAM)
• 細胞内の位置: Cytoplasm: P02213
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 33436.79

構造登録者

Knapp, J.E.,Pahl, R.,Cohen, J.,Nichols, J.C.,Schulten, K.,Gibson, Q.H.,Srajer, V.,Royer Jr., W.E. (登録日: 2009-02-04, 公開日: 2009-12-01, 最終更新日: 2023-09-06)

主引用文献

Knapp, J.E.,Pahl, R.,Cohen, J.,Nichols, J.C.,Schulten, K.,Gibson, Q.H.,Srajer, V.,Royer, W.E.
Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.
Structure, 17:1494-1504, 2009

PubMed Abstract: As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.

PubMed: 19913484
DOI: 10.1016/j.str.2009.09.004

実験手法

X-RAY DIFFRACTION (2.1 Å)