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Title :   OXYGENATED HEMOCYANIN (SUBUNIT TYPE II)

Authors :   B. Hazes, W. G. J. Hol

Date :   17 Oct 95 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Hazes, K. A. Magnus, C. Bonaventura, J. Bonaventura, Z. Dauter, K. H. Kalk, W. G. Hol
Crystal Structure Of Deoxygenated Limulus Polyphemus Subunit Ii Hemocyanin At 2. 18 A Resolution: Clues For A Mechanism For Allosteric Regulation.
Protein Sci. V. 2 597 1993
PubMed-ID: 8518732
(for further references see the PDB file header)

Molecule 1 - HEMOCYANIN (SUBUNIT TYPE II)
	Chains	:	A
	Organism Common	:	ATLANTIC HORSESHOE CRAB
	Organism Scientific	:	LIMULUS POLYPHEMUS
	Organism Taxid	:	6850
	Tissue	:	HEMOLYMPH

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CU	2	Ligand/Ion	COPPER (II) ION
3	NO3	1	Ligand/Ion	NITRATE ION
4	PER	1	Ligand/Ion	PEROXIDE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:173 , HIS A:177 , HIS A:204 , CU A:630 , PER A:631	BINDING SITE FOR RESIDUE CU A 629
2	AC2	SOFTWARE	HIS A:324 , HIS A:328 , HIS A:364 , CU A:629 , PER A:631	BINDING SITE FOR RESIDUE CU A 630
3	AC3	SOFTWARE	SER A:507 , THR A:510 , ASP A:578 , HOH A:781 , HOH A:794	BINDING SITE FOR RESIDUE CA A 632
4	AC4	SOFTWARE	SER A:47 , HIS A:50 , VAL A:329 , ALA A:332 , ARG A:333 , SER A:349	BINDING SITE FOR RESIDUE NO3 A 633
5	AC5	SOFTWARE	PHE A:49 , HIS A:173 , HIS A:177 , HIS A:204 , HIS A:324 , HIS A:328 , PHE A:360 , HIS A:364 , CU A:629 , CU A:630	BINDING SITE FOR RESIDUE PER A 631
6	ANI	AUTHOR	SER A:47 , ARG A:333	BINDING SITE FOR ANIONS (NITRATE AND CHLORIDE BINDING HAS BEEN OBSERVED)
7	CAL	AUTHOR	SER A:507 , THR A:510 , ASP A:578 , HOH A:781 , HOH A:794	BINDING SITE FOR CALCIUM ION. THIS SITE MAY ALSO BIND SODIUM (SEE PDB ENTRY 1LLA)
8	CUA	AUTHOR	HIS A:173 , HIS A:177 , HIS A:204	BINDING SITE FOR COPPER A
9	CUB	AUTHOR	HIS A:324 , HIS A:328 , HIS A:364	BINDING SITE FOR COPPER B

Asymmetric/Biological Unit

No.	Residues
1	A:534	-	A:576
2	A:536	-	A:583

Asymmetric/Biological Unit

No.	Residues
1	Glu A:309	-	Ser A:310
2	Phe A:598	-	Pro A:599

(no "SAP(SNP)/Variant" information available for 1NOL)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMOCYANIN_1	PS00209	Arthropod hemocyanins / insect LSPs signature 1.	HCY2_LIMPO	162-181	1	A:162-181
2	HEMOCYANIN_2	PS00210	Arthropod hemocyanins / insect LSPs signature 2.	HCY2_LIMPO	353-361	1	A:353-361
3	TYROSINASE_2	PS00498	Tyrosinase and hemocyanins CuB-binding region signature.	HCY2_LIMPO	357-368	1	A:357-368

(no "Exon" information available for 1NOL)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:607
 aligned with HCY2_LIMPO | P04253 from UniProtKB/Swiss-Prot  Length:628

    Alignment length:628
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620        
           HCY2_LIMPO     1 TLHDKQIRVCHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKKAHVRPEFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHFTMREQELELKHGINPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGLNEHKSEYCSCGWPSHLLVPKGNIKGMEYHLFVMLTDWDKDKVDGSESVACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFHE 628
               SCOP domains d1nola1 A:1-109 Hemoc        yanin, N-terminal domain                                                        d1nola2 A:110-379 Arthro     pod hemocyanin                                                                                                                                                                                                                                   d1nola3 A:380-628 Arthropod hemocyanin, C-terminal domain                                                                                                                                                                                                 SCOP domains
               CATH domains 1nolA01 A:1-109 Hemoc        yanin, N-terminal domain                                                        1nolA02                      1nolA03   ------1nolA02 A:110-133,A:155-379 Di-copper center containing domain from catechol oxidase                                                                                                                                             1nolA03 A:139-148,A:380-628 E set domains                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh........--------..hhh................hhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhh.......hhhh.hhh...hhhhhhhhhh..-----....eeee.........hhhhhhhhh..hhhhhhhhhhhhh......hhhh......hhhhhhhhhhhhhhhhhhhhhhh...............................................hhhhhhhhhhhhhhhhh.eee.....eee.....hhhhhhhhh........hhhh..hhhhhhhhhh.hhh..........hhh....hhh.hhhhhhhhhhhhhhhhhhhh.....hhhh....eeeeeeeee.....eeeeeeeeeeee............eeeeeeeeee...eeeeeeee.....eeeeeeeeeee..........hhhhhhh.eeeeeeeeee..eeeeeeeehhh..........hhhhh.....----.........hhh.........eeeeeeeeeeehhhh..----.......hhhh.........................hhhh....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANIN_1        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYROSINASE_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nol A   1 TLHDKQIRICHLFEQLSSATV--------HSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKKAH-----DESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHTFMREQELELKHGINPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGL----SEYCSCGWPSHLLVPKGNIKGMEYHLFVMLTDWDKDKV----SVACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFHE 628
                                    10        20|       30        40        50        60        70        80        90       100       110       120       130  |    140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520     |   -|      540       550       560       | -  |    580       590       600       610       620        
                                               21       30                                                                                                    133   139                                                                                                                                                                                                                                                                                                                                                                                                526  531                                  568  573

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "Pfam Domain" information available for 1NOL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HCY2_LIMPO | P04253)

molecular function
	GO:0031404	chloride ion binding	Interacting selectively and non-covalently with chloride ions (Cl-).
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0051259	protein oligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Phe A:598 - Pro A:599	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (9, 9)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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