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(-) Description

Title :  2.9 ANGSTROM CRYSTAL STRUCTURE OF LAMPREY HEMOGLOBIN THAT HAS BEEN EXPOSED TO CARBON MONOXIDE.
 
Authors :  H. A. Heaslet, W. E. Royer Jr.
Date :  15 Jun 00  (Deposition) - 28 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Crystalline Ligand Transitions, Hemoglobin, Heme, Lamprey, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. A. Heaslet, W. E. Royer Jr.
Crystalline Ligand Transitions In Lamprey Hemoglobin. Structural Evidence For The Regulation Of Oxygen Affinity.
J. Biol. Chem. V. 276 26230 2001
PubMed-ID: 11340069  |  Reference-DOI: 10.1074/JBC.M101391200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN V
    ChainsA, B, C, D, E, F
    Organism CommonSEA LAMPREY
    Organism ScientificPETROMYZON MARINUS
    Organism Taxid7757

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CMO6Ligand/IonCARBON MONOXIDE
2HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:51 , PHE A:52 , LYS A:54 , HIS A:73 , ARG A:76 , ALA A:80 , LYS A:104 , HIS A:105 , PHE A:109 , VAL A:111 , TYR A:115 , PHE A:116 , LEU A:119 , LEU A:145 , CMO A:151BINDING SITE FOR RESIDUE HEM A 150
02AC2SOFTWAREHIS A:73 , ILE A:77 , HEM A:150BINDING SITE FOR RESIDUE CMO A 151
03AC3SOFTWAREPHE B:51 , LYS B:54 , HIS B:73 , ARG B:76 , LYS B:104 , HIS B:105 , PHE B:109 , VAL B:111 , TYR B:115 , PHE B:116 , LEU B:119 , LEU B:145 , CMO B:151BINDING SITE FOR RESIDUE HEM B 150
04AC4SOFTWAREHIS B:73 , ILE B:77 , HEM B:150BINDING SITE FOR RESIDUE CMO B 151
05AC5SOFTWAREPHE C:51 , PHE C:52 , LYS C:54 , HIS C:73 , ARG C:76 , ILE C:77 , LEU C:101 , LYS C:104 , HIS C:105 , PHE C:109 , VAL C:111 , TYR C:115 , PHE C:116 , LEU C:145 , CMO C:151BINDING SITE FOR RESIDUE HEM C 150
06AC6SOFTWAREHIS C:73 , ILE C:77 , HEM C:150BINDING SITE FOR RESIDUE CMO C 151
07AC7SOFTWAREPHE D:51 , PHE D:52 , LYS D:54 , HIS D:73 , ARG D:76 , ALA D:80 , LYS D:104 , HIS D:105 , PHE D:109 , TYR D:115 , PHE D:116 , LEU D:119 , LEU D:145 , CMO D:151BINDING SITE FOR RESIDUE HEM D 150
08AC8SOFTWAREHIS D:73 , ILE D:77 , HEM D:150BINDING SITE FOR RESIDUE CMO D 151
09AC9SOFTWAREPHE E:51 , PHE E:52 , LYS E:54 , HIS E:73 , ARG E:76 , LYS E:104 , HIS E:105 , PHE E:109 , VAL E:111 , TYR E:115 , PHE E:116 , LEU E:119 , LEU E:145 , CMO E:151BINDING SITE FOR RESIDUE HEM E 150
10BC1SOFTWAREHIS E:73 , ILE E:77 , HEM E:150BINDING SITE FOR RESIDUE CMO E 151
11BC2SOFTWAREPHE F:51 , PHE F:52 , LYS F:54 , HIS F:73 , ARG F:76 , ILE F:77 , LYS F:104 , HIS F:105 , PHE F:109 , VAL F:111 , TYR F:115 , PHE F:116 , LEU F:145 , CMO F:151BINDING SITE FOR RESIDUE HEM F 150
12BC3SOFTWAREHIS F:73 , ILE F:77 , HEM F:150BINDING SITE FOR RESIDUE CMO F 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLB5_PETMA_001 *T30NGLB5_PETMA  ---  ---A/B/C/D/E/FT29N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLB5_PETMA_001 *T30NGLB5_PETMA  ---  ---A/BT29N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLB5_PETMA_001 *T30NGLB5_PETMA  ---  ---C/DT29N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GLB5_PETMA_001 *T30NGLB5_PETMA  ---  ---E/FT29N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB5_PETMA10-150
 
 
 
 
 
  6A:9-149
B:9-149
C:9-149
D:9-149
E:9-149
F:9-149
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB5_PETMA10-150
 
 
 
 
 
  2A:9-149
B:9-149
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB5_PETMA10-150
 
 
 
 
 
  2-
-
C:9-149
D:9-149
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLB5_PETMA10-150
 
 
 
 
 
  2-
-
-
-
E:9-149
F:9-149

(-) Exons   (0, 0)

(no "Exon" information available for 1F5P)

(-) 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:149
 aligned with GLB5_PETMA | P02208 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           GLB5_PETMA     2 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 150
               SCOP domains d1f5pa_ A: Lamprey globin                                                                                                                             SCOP domains
               CATH domains 1f5pA00 A:1-149 Globins                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: A:9-149 UniProt: 10-150                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5p A   1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with GLB5_PETMA | P02208 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           GLB5_PETMA     2 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 150
               SCOP domains d1f5pb_ B: Lamprey globin                                                                                                                             SCOP domains
               CATH domains 1f5pB00 B:1-149 Globins                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: B:9-149 UniProt: 10-150                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5p B   1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with GLB5_PETMA | P02208 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           GLB5_PETMA     2 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 150
               SCOP domains d1f5pc_ C: Lamprey globin                                                                                                                             SCOP domains
               CATH domains 1f5pC00 C:1-149 Globins                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: C:9-149 UniProt: 10-150                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5p C   1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with GLB5_PETMA | P02208 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           GLB5_PETMA     2 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 150
               SCOP domains d1f5pd_ D: Lamprey globin                                                                                                                             SCOP domains
               CATH domains 1f5pD00 D:1-149 Globins                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: D:9-149 UniProt: 10-150                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5p D   1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain E from PDB  Type:PROTEIN  Length:149
 aligned with GLB5_PETMA | P02208 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           GLB5_PETMA     2 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 150
               SCOP domains d1f5pe_ E: Lamprey globin                                                                                                                             SCOP domains
               CATH domains 1f5pE00 E:1-149 Globins                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: E:9-149 UniProt: 10-150                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5p E   1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain F from PDB  Type:PROTEIN  Length:149
 aligned with GLB5_PETMA | P02208 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           GLB5_PETMA     2 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 150
               SCOP domains d1f5pf_ F: Lamprey globin                                                                                                                             SCOP domains
               CATH domains 1f5pF00 F:1-149 Globins                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: F:9-149 UniProt: 10-150                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5p F   1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F5P)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (GLB5_PETMA | P02208)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLB5_PETMA | P022081f5o 2lhb 3lhb

(-) Related Entries Specified in the PDB File

1f5o 2.9 ANGSTROM CRYSTAL STRUCTURE OF DEOXYGENATED LAMPREY HEMOGLOBIN V IN THE SPACE GROUP P2(1)2(1)2(1)
2lhb REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS.
3lhb 2.7 ANGSTROM CRYSTAL STRUCTURE OF DEOXYGENTATED LAMPREY HEMOGLOBIN V IN THE SPACE GROUP P2(1) WITH TWELVE MONOMERS IN THE ASSYMETRIC UNIT.