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Asym./Biol. Unit (Jmol Viewer)

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Title :   MET-PERCH HEMOGLOBIN AT PH 8.0

Authors :   R. Aranda Iv, H. Cai, E. J. Levin, M. P. Richards, G. N. Phillips Jr.

Date :   02 Dec 07 (Deposition) - 02 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hemoglobin, Autooxidation, Heme Loss, Oxygen Storage/Transport, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Aranda, H. Cai, C. E. Worley, E. J. Levin, R. Li, J. S. Olson, G. N. Phillips, M. P. Richards
Structural Analysis Of Fish Versus Mammalian Hemoglobins: Effect Of The Heme Pocket Environment On Autooxidation And Hemin Loss.
Proteins V. 75 217 2008
PubMed-ID: 18831041 | Reference-DOI: 10.1002/PROT.22236

Molecule 1 - HEMOGLOBIN ALPHA
	Chains	:	A, C
	Organism Common	:	YELLOW PERCH
	Organism Scientific	:	PERCA FLAVESCENS
	Organism Taxid	:	8167

Molecule 2 - HEMOGLOBIN BETA
	Chains	:	B, D
	Organism Common	:	YELLOW PERCH
	Organism Scientific	:	PERCA FLAVESCENS
	Organism Taxid	:	8167

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , PHE A:43 , TRP A:46 , HIS A:59 , THR A:62 , ILE A:63 , LEU A:84 , LEU A:87 , HIS A:88 , LEU A:92 , ASN A:98 , LEU A:102 , VAL A:133 , LEU A:137 , HOH A:150	BINDING SITE FOR RESIDUE HEM A 143
2	AC2	SOFTWARE	LYS A:47 , TYR B:41 , PHE B:42 , PHE B:45 , HIS B:63 , THR B:66 , LEU B:91 , HIS B:92 , LEU B:96 , ASN B:102 , LEU B:141 , HOH B:153	BINDING SITE FOR RESIDUE HEM B 148
3	AC3	SOFTWARE	TYR C:42 , PHE C:43 , HIS C:45 , TRP C:46 , HIS C:59 , THR C:62 , LEU C:84 , HIS C:88 , ASN C:98 , PHE C:99 , LEU C:102 , LEU C:137 , HOH C:145	BINDING SITE FOR RESIDUE HEM C 143
4	AC4	SOFTWARE	TYR D:41 , PHE D:42 , PHE D:45 , HIS D:63 , LEU D:91 , HIS D:92 , LEU D:96 , ASN D:102 , LEU D:106 , LEU D:141 , HOH D:158	BINDING SITE FOR RESIDUE HEM D 148
5	AC5	SOFTWARE	SER A:1 , LYS A:128 , ARG A:135 , HOH A:151 , HOH C:158	BINDING SITE FOR RESIDUE ACE A 0
6	AC6	SOFTWARE	ASN A:78 , GLU A:139	BINDING SITE FOR RESIDUE ACE C 0

(no "SS Bond" information available for 3BJ3)

(no "Cis Peptide Bond" information available for 3BJ3)

(no "SAP(SNP)/Variant" information available for 3BJ3)

(no "PROSITE Motif" information available for 3BJ3)

(no "Exon" information available for 3BJ3)

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:142
 aligned with D0VWS3_PERFV | D0VWS3 from UniProtKB/TrEMBL  Length:142

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
         D0VWS3_PERFV     1 SLSSKDKDAVKALWGKIADKAEEIGADALGRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGLVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVQLAVKFPKDFTPEVHLSYDKFFSAVARALAEKYR 142
               SCOP domains d3bj3a_ A: automated matches                                                                                                                   SCOP domains
               CATH domains 3bj3A00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bj3 A   1 SLSSKDKDAVKALWGKIADKAEEIGADALGRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGLVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVQLAVKFPKDFTPEVHLSYDKFFSAVARALAEKYR 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with D0VWV3_PERFV | D0VWV3 from UniProtKB/TrEMBL  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
         D0VWV3_PERFV     1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
               SCOP domains d3bj3b_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 3bj3B00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bj3 B   1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with D0VWS3_PERFV | D0VWS3 from UniProtKB/TrEMBL  Length:142

    Alignment length:143
                                                                                                                                                                       142 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 | 
         D0VWS3_PERFV     1 SLSSKDKDAVKALWGKIADKAEEIGADALGRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGLVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVQLAVKFPKDFTPEVHLSYDKFFSAVARALAEKYR-   -
               SCOP domains d3bj3c_ C: automated matches                                                                                                                    SCOP domains
               CATH domains 3bj3C00 C:1-142 Globins                                                                                                                       - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bj3 C   1 SLSSKDKDAVKALWGKIADKAEEIGADALGRMLAVYPQTKTYFSHWKDLSPGSAPVNKHGKTIMGGLVDAVASIDDLNAGLLALSELHAFTLRVDPANFKILSHCILVQLAVKFPKDFTPEVHLSYDKFFSAVARALAEKYRx   0
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 ||
                                                                                                                                                                       142|
                                                                                                                                                                          0-ACE

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with D0VWV3_PERFV | D0VWV3 from UniProtKB/TrEMBL  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
         D0VWV3_PERFV     1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
               SCOP domains d3bj3d_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 3bj3D00 D:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bj3 D   1 VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLYNAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVDPDNFKLLSDCLTIVVAAQLGKAFSGEVQAAFQKFLSVVVSALGKQYH 146
                                    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 '\|'

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: automated matches (99)

Yellow perch (Perca flavescens) [TaxId: 8167] (3)

1a	d3bj3a_	A:
1b	d3bj3c_	C:

Protein domain: Hemoglobin, beta-chain (292)

Yellow perch (Perca flavescens) [TaxId: 8167] (4)

2a	d3bj3b_	B:
2b	d3bj3d_	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)

Yellow perch (Perca flavescens) (4)

1a	3bj3B00	B:1-146
1b	3bj3A00	A:1-142
1c	3bj3C00	C:1-142
1d	3bj3D00	D:1-146

(no "Pfam Domain" information available for 3BJ3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (D0VWS3_PERFV | D0VWS3)

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 (D0VWV3_PERFV | D0VWV3)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bj3)

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	3bj3
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	D0VWS3_PERFV \| D0VWS3
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		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	D0VWV3_PERFV \| D0VWV3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
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	D0VWS3_PERFV \| D0VWS3
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	D0VWV3_PERFV \| D0VWV3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	D0VWS3_PERFV \| D0VWS3	:	3bj1 3bj2
	D0VWV3_PERFV \| D0VWV3	:	1xq5 3bj1 3bj2

3bj1	MET-PERCH HEMOLGOBIN AT PH 5.7
3bj2	MET-PERCH HEMOLGOBIN AT PH 6.3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (8, 16)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File