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(-) Description

Title :  HYDROXO BRIDGE MET FORM HEMOCYANIN FROM LIMULUS
 
Authors :  S. Liu, K. Magnus
Date :  17 Mar 97  (Deposition) - 20 Aug 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Oxygen Transport, Respiratory Protein, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, H. Ton-That, K. Magnus
Crystallographic Studies Of Hydroxo, Nitrosyl, Azido And Fluro Met Form Hemocyanin Subunit Ii From Limulus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METCYANIN II
    Chains: A
    Organism Common: ATLANTIC HORSESHOE CRAB
    Organism Scientific: LIMULUS POLYPHEMUS
    Organism Taxid: 6850
    Other Details: HEMOCYANIN TREATED BY EXCESSIVE AMOUNT OF H2O2
    Other Details - Source: FROM HEMOLYMPH
    Synonym: BIS(M-HYDROXO) MET FORM METCYANIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CU2Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:324 , HIS A:328 , HIS A:364 , CU A:630 , HOH A:675 , HOH A:730BINDING SITE FOR RESIDUE CU A 629
2AC2SOFTWAREHIS A:173 , HIS A:177 , HIS A:204 , CU A:629 , HOH A:675 , HOH A:730BINDING SITE FOR RESIDUE CU A 630
3AC3SOFTWARESER A:47 , ARG A:333 , SER A:349BINDING SITE FOR RESIDUE CL A 631
4CU2UNKNOWNHIS A:173 , HIS A:177 , HIS A:204 , HIS A:324 , HIS A:328 , HIS A:364DESCRIPTION NOT PROVIDED

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:598 -Pro A:599

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LL1)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOCYANIN_1PS00209 Arthropod hemocyanins / insect LSPs signature 1.HCY2_LIMPO162-181  1A:162-181
2HEMOCYANIN_2PS00210 Arthropod hemocyanins / insect LSPs signature 2.HCY2_LIMPO353-361  1A:353-361
3TYROSINASE_2PS00498 Tyrosinase and hemocyanins CuB-binding region signature.HCY2_LIMPO357-368  1A:357-368
Biological Unit 1 (3, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOCYANIN_1PS00209 Arthropod hemocyanins / insect LSPs signature 1.HCY2_LIMPO162-181  6A:162-181
2HEMOCYANIN_2PS00210 Arthropod hemocyanins / insect LSPs signature 2.HCY2_LIMPO353-361  6A:353-361
3TYROSINASE_2PS00498 Tyrosinase and hemocyanins CuB-binding region signature.HCY2_LIMPO357-368  6A:357-368

(-) Exons   (0, 0)

(no "Exon" information available for 1LL1)

(-) Sequences/Alignments

Asymmetric 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:590
 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 d1ll1a1 A:1-109 Hemocy          anin, N-terminal domain                                                      d1ll1a2 A:110-379 Arth           ropod    hemocyanin                                                                                                                                                                                                                          d1ll1a3 A:380-628 Arthropod hemocyanin, C-terminal domain                                                                                                                                                                                                 SCOP domains
               CATH domains 1ll1A01 A:1-109 Hemocy          anin, N-terminal domain                                                      1ll1A02                          1ll1A   1ll1A02 A:110-131,A:151-377 Di-copper center containing domain from catechol oxidase                                                                                                                                               1ll1A03 A:143-147,A:378-628 E set domains                                                                                                                                                                                                                   CATH domains
               Pfam domains Hemocyanin_N-1ll1A03 A          :1-106                                                                    ---Hemocyanin_M-1ll1A01 A           :110-   373                                                                                                                                                                                                                            -----Hemocyanin_C-1ll1A02 A:379-627                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author ..hhhhhhhhhh.........h----------hh................hhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhh...........hhhh.hhh...hhhhhh....-----------eeee.---.....hhhhhhhhh..hhhhhhhhhhhhh......hhhh......hhhhhhhhhhhhhhhhhhhhhh................................................hhhhhhhhhhhhhhhhh.eee.....eee.....hhhhhhhhh........hhhh..hhhhhhhhhh.hhh..........hhh....hhh.hhhhhhhhhhhhhhhhhhhh.....hhhh....eeeeeeeee.....eeeeeeeee...............eeeeeeeeee...eeeeeeee.....eeeeeeeeeee..........hhhh....eeeeeeeeee..eeeeeeeehhh..........hhhh.---------.........hhh.........eeeeeeeeeeehhhh..-----......hhhh.........................hhh.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANIN_1        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOCYANI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYROSINASE_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ll1 A   1 TLHDKQIRVCHLFEQLSSATVI----------RLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKK-----------ILVDV---GNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHGTDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHTFMREQELELKHGINPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELRRTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLL---------SEYCSCGWPSHLLVPKGNIKGMEYHLFVMLTDWDKDKV-----VACVDAVSYCGARDHKYPDKKPMGFPFDRPIHTEHISDFLTNNMFIKDIKIKFHE 628
                                    10        20 |       -  |     40        50        60        70        80        90       100       110       120       130|        -  |   |  -|      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        
                                                22         33                                                                                               131         143 147 151                                                                                                                                                                                                                                                                                                                                                                               521       531                                  568   574
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: Di-copper (13)
(-)
Clan: no clan defined [family: Hemocyanin_C] (3)
(-)
Clan: no clan defined [family: Hemocyanin_N] (3)

(-) Gene Ontology  (12, 12)

Asymmetric 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HCY2_LIMPO | P04253: 1lla 1nol 1oxy

(-) Related Entries Specified in the PDB File

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