2d2m
From Proteopedia
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|PDB= 2d2m |SIZE=350|CAPTION= <scene name='initialview01'>2d2m</scene>, resolution 2.85Å | |PDB= 2d2m |SIZE=350|CAPTION= <scene name='initialview01'>2d2m</scene>, resolution 2.85Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene> | + | |LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2d2n|2D2N]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2m OCA], [http://www.ebi.ac.uk/pdbsum/2d2m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d2m RCSB]</span> | ||
}} | }} | ||
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[[Category: Numoto, N.]] | [[Category: Numoto, N.]] | ||
[[Category: Sasayama, Y.]] | [[Category: Sasayama, Y.]] | ||
| - | [[Category: HEM]] | ||
| - | [[Category: OXY]] | ||
[[Category: giant hemoglobin]] | [[Category: giant hemoglobin]] | ||
[[Category: invertebrate]] | [[Category: invertebrate]] | ||
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[[Category: sulfide binding]] | [[Category: sulfide binding]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:29:29 2008'' |
Revision as of 23:29, 30 March 2008
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| , resolution 2.85Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Related: | 2D2N
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi
Overview
Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.
About this Structure
2D2M is a Protein complex structure of sequences from Oligobrachia mashikoi. Full crystallographic information is available from OCA.
Reference
Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi., Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K, Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14521-6. Epub 2005 Oct 3. PMID:16204001
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