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Asym./Biol. Unit (Jmol Viewer)

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Title :   CO FORM HEMOGLOBIN FROM MUSTELUS GRISEUS

Authors :   Y. Naoi, K. T. Chong, K. Yoshimatsu, G. Miyazaki, J. R. H. Tame, S. Y. Park, S. I. Adachi, H. Morimoto

Date :   08 Aug 00 (Deposition) - 06 Sep 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Hemoglobin, Carbon Monoxide Bound Form, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Naoi, K. T. Chong, K. Yoshimatsu, G. Miyazaki, J. R. Tame, S. Y. Park, S. Adachi, H. Morimoto
The Functional Similarity And Structural Diversity Of Human And Cartilaginous Fish Hemoglobins.
J. Mol. Biol. V. 307 259 2001
PubMed-ID: 11243818 | Reference-DOI: 10.1006/JMBI.2000.4446
(for further references see the PDB file header)

Molecule 1 - PROTEIN (HEMOGLOBIN)
	Cell	:	RED BLOOD CELL
	Chains	:	A, C
	Fragment	:	ALPHA CHAIN
	Organism Scientific	:	MUSTELUS GRISEUS
	Organism Taxid	:	89020
	Tissue	:	BLOOD

Molecule 2 - PROTEIN (HEMOGLOBIN)
	Cell	:	RED BLOOD CELL
	Chains	:	B, D
	Fragment	:	BETA CHAIN
	Organism Scientific	:	MUSTELUS GRISEUS
	Organism Taxid	:	89020
	Tissue	:	BLOOD

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CMO	4	Ligand/Ion	CARBON MONOXIDE
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , PHE A:43 , HIS A:58 , LYS A:61 , ALA A:65 , HIS A:87 , LEU A:91 , ASN A:97 , PHE A:98 , LEU A:101 , CYS A:132 , LEU A:135 , CMO A:142 , LYS B:13	BINDING SITE FOR RESIDUE HEM A 141
2	AC2	SOFTWARE	HIS A:58 , VAL A:62 , HEM A:141	BINDING SITE FOR RESIDUE CMO A 142
3	AC3	SOFTWARE	MET B:31 , TYR B:41 , PHE B:42 , HIS B:53 , LEU B:78 , HIS B:82 , LEU B:86 , VAL B:88 , SER B:92 , PHE B:93 , ILE B:131 , CMO B:137	BINDING SITE FOR RESIDUE HEM B 136
4	AC4	SOFTWARE	HIS B:53 , VAL B:57 , HEM B:136	BINDING SITE FOR RESIDUE CMO B 137
5	AC5	SOFTWARE	TYR C:42 , PHE C:43 , HIS C:58 , LEU C:83 , HIS C:87 , LEU C:91 , ASN C:97 , PHE C:98 , LEU C:101 , LEU C:135 , CMO C:142 , HOH C:1055	BINDING SITE FOR RESIDUE HEM C 141
6	AC6	SOFTWARE	HIS C:58 , VAL C:62 , HEM C:141	BINDING SITE FOR RESIDUE CMO C 142
7	AC7	SOFTWARE	TYR D:41 , PHE D:42 , HIS D:53 , ILE D:56 , LYS D:81 , HIS D:82 , SER D:92 , PHE D:93 , LEU D:96 , ILE D:131 , CMO D:137	BINDING SITE FOR RESIDUE HEM D 136
8	AC8	SOFTWARE	HIS D:53 , VAL D:57 , HEM D:136	BINDING SITE FOR RESIDUE CMO D 137

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

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

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBA_MUSGR	15-141	2	A:14-140 C:14-140
1	GLOBIN	PS01033	Globin family profile.	HBB_MUSGR	16-137	2	B:15-133 D:15-133

(no "Exon" information available for 1GCW)

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:140
 aligned with HBA_MUSGR | Q9YGW2 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
            HBA_MUSGR     2 AFTACEKQTIGKIAQVLAKSPEAYGAECLARLFVTHPGSKSYFEYKDYSAAGAKVQVHGGKVIRAVVKAAEHVDDLHSHLETLALTHGKKLLVDPQNFPMLSECIIVTLATHLTEFSPDTHCAVDKLLSAICQELSSRYR 141
               SCOP domains d1gcwa_ A: Hemoglobin, alpha-chain                                                                                                           SCOP domains
               CATH domains 1gcwA00 A:1-140 Globins                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GLOBIN  PDB: A:14-140 UniProt: 15-141                                                                                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gcw A   1 AFTACEKQTIGKIAQVLAKSPEAYGAECLARLFVTHPGSKSYFEYKDYSAAGAKVQVHGGKVIRAVVKAAEHVDDLHSHLETLALTHGKKLLVDPQNFPMLSECIIVTLATHLTEFSPDTHCAVDKLLSAICQELSSRYR 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with HBB_MUSGR | Q9YGW1 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
            HBB_MUSGR     2 VHWTQEERDEISKTFQGTDMKTVVTQALDRMFKVYPWTNRYFQKRTDFRSSIHAGIVVGALQDAVKHMDDVKTLFKDLSKKHADDLHVDPGSFHLLTDCIIVELAYLRKDCFTPHIQGIWDKFFEVVIDAISK 134
               SCOP domains d1gcwb_ B: Hemoglobin, beta-chain                                                                                                     SCOP domains
               CATH domains 1gcwB00 B:1-133 Globins                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------GLOBIN  PDB: B:15-133 UniProt: 16-137                                                                                   PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gcw B   1 VHWTQEERDEISKTFQGTDMKTVVTQALDRMFKVYPWTNRYFQ----FRSSIHAGIVVGALQDAVKHMDDVKTLFKDLSKKHADDLHVDPGSFHLLTDCIIVELAYLRKDCFTPHIQGIWDKFFEVVIDAISK 133
                                    10        20        30        40  |    |50        60        70        80        90       100       110       120       130   
                                                                     43   48

Chain C from PDB  Type:PROTEIN  Length:140
 aligned with HBA_MUSGR | Q9YGW2 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
            HBA_MUSGR     2 AFTACEKQTIGKIAQVLAKSPEAYGAECLARLFVTHPGSKSYFEYKDYSAAGAKVQVHGGKVIRAVVKAAEHVDDLHSHLETLALTHGKKLLVDPQNFPMLSECIIVTLATHLTEFSPDTHCAVDKLLSAICQELSSRYR 141
               SCOP domains d1gcwc_ C: Hemoglobin, alpha-chain                                                                                                           SCOP domains
               CATH domains 1gcwC00 C:1-140 Globins                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GLOBIN  PDB: C:14-140 UniProt: 15-141                                                                                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gcw C   1 AFTACEKQTIGKIAQVLAKSPEAYGAECLARLFVTHPGSKSYFEYKDYSAAGAKVQVHGGKVIRAVVKAAEHVDDLHSHLETLALTHGKKLLVDPQNFPMLSECIIVTLATHLTEFSPDTHCAVDKLLSAICQELSSRYR 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with HBB_MUSGR | Q9YGW1 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
            HBB_MUSGR     2 VHWTQEERDEISKTFQGTDMKTVVTQALDRMFKVYPWTNRYFQKRTDFRSSIHAGIVVGALQDAVKHMDDVKTLFKDLSKKHADDLHVDPGSFHLLTDCIIVELAYLRKDCFTPHIQGIWDKFFEVVIDAISK 134
               SCOP domains d1gcwd_ D: Hemoglobin, beta-chain                                                                                                     SCOP domains
               CATH domains 1gcwD00 D:1-133 Globins                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------GLOBIN  PDB: D:15-133 UniProt: 16-137                                                                                   PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gcw D   1 VHWTQEERDEISKTFQGTDMKTVVTQALDRMFKVYPWTNRYFQ----FRSSIHAGIVVGALQDAVKHMDDVKTLFKDLSKKHADDLHVDPGSFHLLTDCIIVELAYLRKDCFTPHIQGIWDKFFEVVIDAISK 133
                                    10        20        30        40  |    |50        60        70        80        90       100       110       120       130   
                                                                     43   48

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: Hemoglobin, alpha-chain (292)

Houndshark (Mustelus griseus) [TaxId: 89020] (2)

1a	d1gcwa_	A:
1b	d1gcwc_	C:

Protein domain: Hemoglobin, beta-chain (292)

Houndshark (Mustelus griseus) [TaxId: 89020] (2)

2a	d1gcwb_	B:
2b	d1gcwd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Mustelus griseus. Organism_taxid: 89020. (2)

1a	1gcwA00	A:1-140
1b	1gcwC00	C:1-140
1c	1gcwB00	B:1-133
1d	1gcwD00	D:1-133

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA_MUSGR | Q9YGW2)

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.
cellular component
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B,D (HBB_MUSGR | Q9YGW1)

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.

Asymmetric/Biological Unit
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	HBA_MUSGR \| Q9YGW2	:	1gcv
	HBB_MUSGR \| Q9YGW1	:	1gcv

1gcv	1GCV CONTAINS THE DEOXY FORM OF HEMOGLOBIN.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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