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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF HBII-OXY FROM LUCINA PECTINATA AT PH 4.0
 
Authors :  J. A. Gavira, C. A. Nieves-Marrero, C. R. Ruiz-Martinez, R. A. Estremer Andujar, J. Lopez-Garriga, J. M. Garcia-Ruiz
Date :  05 Nov 10  (Deposition) - 09 Nov 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.17
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (4x)
Keywords :  Ph Behavior, Oxygen Carrier, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Nieves-Marrero, C. R. Ruiz-Martinez, R. A. Estremera-Andujar, J. Lopez-Garriga, J. M. Garcia-Ruiz, J. A. Gavira
Ph-Dependence Crystallographic Studies Of The Oxygen Carrie Hemoglobin Ii From Lucina Pectinata
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN II
    ChainsA, B
    Organism CommonLUCINA PECTINATA
    Organism ScientificPHACOIDES PECTINATUS
    Organism Taxid244486

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB
Biological Unit 3 (2x)AB
Biological Unit 4 (4x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 4 (2, 16)
No.NameCountTypeFull Name
1ACE8Mod. Amino AcidACETYL GROUP
2HEM8Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:40 , PRO A:43 , PHE A:44 , LEU A:47 , GLN A:65 , VAL A:68 , PHE A:69 , LEU A:96 , HIS A:97 , ARG A:100 , LEU A:107 , ALA A:110 , TYR A:111 , HOH A:501 , LYS B:92 , LYS B:95 , LEU B:96BINDING SITE FOR RESIDUE HEM A 500
2AC2SOFTWARELYS A:92 , LYS A:95 , LEU A:96 , PRO B:43 , LEU B:47 , GLN B:65 , VAL B:68 , PHE B:69 , MET B:93 , LEU B:96 , HIS B:97 , ARG B:100 , ILE B:102 , LEU B:107 , ALA B:110 , TYR B:111 , HOH B:501BINDING SITE FOR RESIDUE HEM B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PI4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PI4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PI4)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB2_PHAPT4-143
 
  2A:3-143
B:3-143
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB2_PHAPT4-143
 
  2A:3-143
B:3-143
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB2_PHAPT4-143
 
  4A:3-143
B:3-143
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB2_PHAPT4-143
 
  4A:3-143
B:3-143
Biological Unit 4 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB2_PHAPT4-143
 
  8A:3-143
B:3-143

(-) Exons   (0, 0)

(no "Exon" information available for 3PI4)

(-) 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:152
 aligned with GLB2_PHAPT | P41261 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:152
                                                                                                                85                                                                  
                                                                                                              84 |                                                                  
                                    10        20        30        40        50        60        70        80   | |  89        99       109       119       129       139       149  
           GLB2_PHAPT     1 MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDN-MLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
               SCOP domains d3pi4a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: A:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi4 A   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            |                                                                                                                                                       
                            0-ACE                                                                                                                                                   

Chain A from PDB  Type:PROTEIN  Length:152
 aligned with Q86G74_PHAPT | Q86G74 from UniProtKB/TrEMBL  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
         Q86G74_PHAPT     1 MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 152
               SCOP domains d3pi4a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi4 A   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with GLB2_PHAPT | P41261 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:152
                                                                                                                85                                                                  
                                                                                                              84 |                                                                  
                                    10        20        30        40        50        60        70        80   | |  89        99       109       119       129       139       149  
           GLB2_PHAPT     1 MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDN-MLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
               SCOP domains d3pi4b_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: B:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi4 B   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with Q86G74_PHAPT | Q86G74 from UniProtKB/TrEMBL  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
         Q86G74_PHAPT     1 MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 152
               SCOP domains d3pi4b_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi4 B   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE                                                                                                                                                   

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PI4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PI4)

(-) Gene Ontology  (7, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q86G74_PHAPT | Q86G74)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    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: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.

Chain A,B   (GLB2_PHAPT | P41261)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLB2_PHAPT | P412612olp 3pi1 3pi2 3pi3 3pt7 3pt8
        Q86G74_PHAPT | Q86G742olp 3pi1 3pi2 3pi3 3pt7 3pt8

(-) Related Entries Specified in the PDB File

2olp 3pi1 3pi2 3pi3