2H8D - JenaLib

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Title :   CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN FROM TREMATOMUS BERNACCHII AT PH 8.4

Authors :   L. Mazzarella, A. Vergara, L. Vitagliano, A. Merlino, G. Bonomi, S. Scala, C. Verde, G. Di Prisco

Date :   07 Jun 06 (Deposition) - 29 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

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

Keywords :   Root Effect, Ph, Cooperativity, Hemoglobin, Allostery, High Resolution, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Mazzarella, A. Vergara, L. Vitagliano, A. Merlino, G. Bonomi, S. Scala, C. Verde, G. Di Prisco
High Resolution Crystal Structure Of Deoxy Hemoglobin From Trematomus Bernacchii At Different Ph Values: The Role Of Histidine Residues In Modulating The Strength Of The Root Effect.
Proteins V. 65 490 2006
PubMed-ID: 16909420 | Reference-DOI: 10.1002/PROT.21114
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN ALPHA SUBUNIT
	Chains	:	A, C
	Organism Common	:	EMERALD ROCKCOD
	Organism Scientific	:	TREMATOMUS BERNACCHII
	Organism Taxid	:	40690
	Synonym	:	HEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN

Molecule 2 - HEMOGLOBIN BETA SUBUNIT
	Chains	:	B, D
	Organism Common	:	EMERALD ROCKCOD
	Organism Scientific	:	TREMATOMUS BERNACCHII
	Organism Taxid	:	40690
	Synonym	:	HEMOGLOBIN BETA CHAIN, BETA-GLOBIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:13 , HIS B:17 , ASP C:75 , HOH C:1375 , HOH C:1376 , HOH C:1380	BINDING SITE FOR RESIDUE K C 1001
2	AC2	SOFTWARE	ASP A:75 , HOH A:1378 , HOH A:1379 , ASP D:13 , HIS D:17	BINDING SITE FOR RESIDUE K A 1002
3	AC3	SOFTWARE	TYR A:42 , PHE A:43 , HIS A:45 , TRP A:46 , HIS A:59 , LYS A:62 , VAL A:63 , HIS A:88 , LEU A:92 , VAL A:94 , ASN A:98 , LEU A:102 , HOH A:1061 , HOH A:1361	BINDING SITE FOR RESIDUE HEM A 200
4	AC4	SOFTWARE	THR B:38 , HIS B:41 , PHE B:42 , HIS B:63 , VAL B:67 , LEU B:91 , HIS B:92 , LEU B:96 , PHE B:103	BINDING SITE FOR RESIDUE HEM B 400
5	AC5	SOFTWARE	TYR C:42 , PHE C:43 , HIS C:45 , TRP C:46 , HIS C:59 , LYS C:62 , VAL C:63 , LEU C:84 , HIS C:88 , LEU C:92 , ASN C:98 , PHE C:99 , LEU C:102 , HOH C:1264 , HOH C:1328	BINDING SITE FOR RESIDUE HEM C 600
6	AC6	SOFTWARE	THR D:38 , HIS D:63 , LYS D:66 , VAL D:67 , HIS D:92 , LEU D:96 , ASN D:102 , PHE D:103 , LEU D:141	BINDING SITE FOR RESIDUE HEM D 800

(no "SS Bond" information available for 2H8D)

(no "Cis Peptide Bond" information available for 2H8D)

(no "SAP(SNP)/Variant" information available for 2H8D)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBA_TREBE	2-142	2	A:2-142 C:2-142
1	GLOBIN	PS01033	Globin family profile.	HBB_TREBE	5-147	2	B:4-146 D:4-146

(no "Exon" information available for 2H8D)

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:143
 aligned with HBA_TREBE | P80043 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
            HBA_TREBE     - -SLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d2h8da_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -2h8dA00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8d A   0 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            |                                                                                                                                              
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB_TREBE | P80044 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_TREBE     2 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 147
               SCOP domains d2h8db_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2h8dB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 5-147                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8d B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 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 HBA_TREBE | P80043 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
            HBA_TREBE     - -SLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d2h8dc_ C: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -2h8dC00 C:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: C:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8d C   0 xSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPANFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139   
                            0-ACE

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with HBB_TREBE | P80044 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_TREBE     2 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 147
               SCOP domains d2h8dd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2h8dD00 D:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: D:4-146 UniProt: 5-147                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8d D   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLYNAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAVVVSALGKQYH 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: Hemoglobin, alpha-chain (292)

Emerald rockcod (Pagothenia bernacchii) [TaxId: 40690] (11)

1a	d2h8da_	A:
1b	d2h8dc_	C:

Protein domain: Hemoglobin, beta-chain (292)

Emerald rockcod (Pagothenia bernacchii) [TaxId: 40690] (11)

2a	d2h8db_	B:
2b	d2h8dd_	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)

Emerald rockcod (Trematomus beRNAcchii) (8)

1a	2h8dB00	B:1-146
1b	2h8dA00	A:1-142
1c	2h8dC00	C:1-142
1d	2h8dD00	D:1-146

(no "Pfam Domain" information available for 2H8D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA_TREBE | P80043)

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_TREBE | P80044)

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 2h8d)

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2aa1	CRYSTAL STRUCTURE OF THE CATHODIC HEMOLGLOBIN ISOLATED FROM THE ANTARCTIC FISH TREMATOMUS NEWNESI
2h8f	CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN FROM TREMATOMUS BERNACCHII AT PH 6.2

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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