3GKV - JenaLib

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Title :   X-RAY STRUCTURE OF AN INTERMEDIATE ALONG THE OXIDATION PATHWAY OF TREMATOMUS BERNACCHII HEMOGLOBIN

Authors :   A. Merlino, L. Vitagliano, F. Sica, A. Vergara, L. Mazzarella

Date :   11 Mar 09 (Deposition) - 05 May 09 (Release) - 03 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Hemoglobin, Intermediate Quaternary Structure, , Acetylation, Heme, Iron, Metal-Binding, Oxygen Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Merlino, L. Vitagliano, B. D. Howes, C. Verde, G. Di Prisco, G. Smulevich, F. Sica, A. Vergara
Combined Crystallographic And Spectroscopic Analysis Of Trematomus Bernacchii Hemoglobin Highlights Analogies And Differences In The Peculiar Oxidation Pathway Of Antarctic Fish Hemoglobins
Biopolymers V. 91 1117 2009
PubMed-ID: 19373928 | Reference-DOI: 10.1002/BIP.21206
(for further references see the PDB file header)

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

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

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

Biological Unit 1 (3, 10)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , PHE A:43 , HIS A:45 , TRP A:46 , HIS A:59 , LYS A:62 , GLN A:87 , HIS A:88 , LEU A:92 , VAL A:94 , ASN A:98 , LEU A:102 , ASN A:103 , LEU A:137 , CMO A:199 , HOH A:1103 , HOH A:1291	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	HIS B:41 , PHE B:42 , HIS B:63 , LYS B:66 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , CMO B:399 , HOH B:1265	BINDING SITE FOR RESIDUE HEM B 400
3	AC3	SOFTWARE	LEU A:29 , HIS A:59 , VAL A:63 , HEM A:200 , HOH A:1290 , HOH A:1291	BINDING SITE FOR RESIDUE CMO A 199
4	AC4	SOFTWARE	HIS B:63 , VAL B:67 , HEM B:400	BINDING SITE FOR RESIDUE CMO B 399

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

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

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

Asymmetric Unit (1, 2)

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

Biological Unit 1 (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
1	GLOBIN	PS01033	Globin family profile.	HBB_TREBE	5-147	2	B:4-146

(no "Exon" information available for 3GKV)

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
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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 d3gkva_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains -3gkvA00 A:1-142 Globins                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gkv 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 d3gkvb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 3gkvB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 5-147                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gkv B   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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

d3gkva_

Protein domain: Hemoglobin, beta-chain (292)

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

d3gkvb_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Emerald rockcod (Trematomus beRNAcchii) (8)

1a	3gkvB00	B:1-146
1b	3gkvA00	A:1-142

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

Asymmetric Unit(hide GO term definitions)

Chain A (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 (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 Unit
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(no "Cis Peptide Bonds" information available for 3gkv)

Biological Unit
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(no "Related Entries Specified in the PDB File" available for 3GKV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

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