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(-) Description

Title :  STRUCTURE AND LIGAND SELECTION OF HEMOGLOBIN II FROM LUCINA PECTINATA
 
Authors :  J. A. Gavira, A. Camara-Artigas, W. De Jesus, J. Lopez-Garriga, J. M. G Ruiz
Date :  19 Jan 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxygen Transport, Hemoprotein, Globins, Oxygen Storage-Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Gavira, A. Camara-Artigas, W. De Jesus-Bonilla, J. Lopez-Garriga, A. Lewis, R. Pietri, S. R. Yeh, C. L. Cadilla, J. M. Garcia-Ruiz
Structure And Ligand Selection Of Hemoglobin Ii From Lucina Pectinata
J. Biol. Chem. V. 283 9414 2008
PubMed-ID: 18203714  |  Reference-DOI: 10.1074/JBC.M705026200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN II
    Chains: A, B
    Organism Scientific: LUCINA PECTINATA
    Organism Taxid: 29163

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY2Ligand/IonOXYGEN MOLECULE
4SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC3SOFTWAREHIS A:37 , HOH A:549 , THR B:1 , LYS B:8 , ASN B:83 , HOH B:533 , HOH B:538 , HOH B:593BINDING SITE FOR RESIDUE SO4 B 200
2AC4SOFTWAREARG A:12 , SER A:16 , HOH A:519 , HOH A:523 , HOH A:586BINDING SITE FOR RESIDUE SO4 A 200
3AC5SOFTWAREPRO A:43 , PHE A:44 , LEU A:47 , GLN A:65 , MET A:93 , LEU A:96 , HIS A:97 , ARG A:100 , ILE A:102 , LEU A:107 , ALA A:110 , TYR A:111 , HOH A:504 , HOH A:505 , HOH A:506 , HOH A:520 , HOH A:526 , HOH A:535 , LYS B:92BINDING SITE FOR RESIDUE HEM A 500
4AC6SOFTWARETYR A:30 , PHE A:44 , GLN A:65BINDING SITE FOR RESIDUE OXY A 501
5AC7SOFTWARELYS A:92 , PRO B:43 , PHE B:44 , LEU B:47 , GLN B:65 , PHE B:69 , LEU B:96 , HIS B:97 , ARG B:100 , ILE B:102 , LEU B:107 , TYR B:111 , HOH B:502 , HOH B:503 , HOH B:504 , HOH B:505 , HOH B:516 , HOH B:565BINDING SITE FOR RESIDUE HEM B 500
6AC8SOFTWARETYR B:30 , GLN B:65BINDING SITE FOR RESIDUE OXY B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OLP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OLP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OLP)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OLP)

(-) Sequences/Alignments

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
(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 d2olpa_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhh....hhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: A:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olp 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 d2olpa_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhh....hhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olp 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 d2olpb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Globin-2olpB01 B:7-115                                                                                       ------------------------------------ Pfam domains (1)
           Pfam domains (2) -------Globin-2olpB02 B:7-115                                                                                       ------------------------------------ Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: B:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olp 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 d2olpb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Globin-2olpB01 B:7-115                                                                                       ------------------------------------ Pfam domains (1)
           Pfam domains (2) -------Globin-2olpB02 B:7-115                                                                                       ------------------------------------ Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olp 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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OLP)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLB2_PHAPT | P41261: 3pi1 3pi2 3pi3 3pi4 3pt7 3pt8
        Q86G74_PHAPT | Q86G74: 3pi1 3pi2 3pi3 3pi4 3pt7 3pt8

(-) Related Entries Specified in the PDB File

1bob HBI FROM THE CLAM LUCINA PECTINATA, CYANIDE COMPLEX
1ebt HBI FROM THE CLAM LUCINA PECTINATA, CYANIDE COMPLEX
1flp HBI FROM LUCINA PECTINATA,MONOMERIC
1moh HBI FROM LUCINA PECTINATA,MONOMERIC