3VHB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   IMIDAZOLE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA SP.

Authors :   M. Bolognesi, A. Boffi, M. Coletta, A. Mozzarelli, A. Pesce, C. Tarricone, P. Ascenzi

Date :   17 Mar 99 (Deposition) - 18 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hemoprotein, Oxygen Transport, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Bolognesi, A. Boffi, M. Coletta, A. Mozzarelli, A. Pesce, C. Tarricone, P. Ascenzi
Anticooperative Ligand Binding Properties Of Recombinant Ferric Vitreoscilla Homodimeric Hemoglobin: A Thermodynamic, Kinetic And X-Ray Crystallographic Study.
J. Mol. Biol. V. 291 637 1999
PubMed-ID: 10448042 | Reference-DOI: 10.1006/JMBI.1999.2975
(for further references see the PDB file header)

Molecule 1 - PROTEIN (HEMOGLOBIN)
	Atcc	:	ATCC 15218
	Chains	:	A, B
	Collection	:	ATCC 15218
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	VGB
	Expression System Plasmid	:	PDH88
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Organism Scientific	:	VITREOSCILLA STERCORARIA
	Organism Taxid	:	61
	Strain	:	C1
	Synonym	:	SOLUBLE CYTOCHROME O

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	IMD	2	Ligand/Ion	IMIDAZOLE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:42 , PHE A:43 , LEU A:57 , THR A:60 , LYS A:84 , HIS A:85 , VAL A:90 , HIS A:94 , TYR A:95 , VAL A:98 , TYR A:126 , IMD A:160 , HOH A:214	BINDING SITE FOR RESIDUE HEM A 150
2	AC2	SOFTWARE	TYR A:29 , PRO A:54 , LEU A:57 , HEM A:150	BINDING SITE FOR RESIDUE IMD A 160
3	AC3	SOFTWARE	LEU B:42 , PHE B:43 , LEU B:57 , THR B:60 , ILE B:81 , LYS B:84 , HIS B:85 , ALA B:88 , VAL B:90 , HIS B:94 , TYR B:95 , VAL B:98 , PHE B:133 , IMD B:170 , HOH B:200 , HOH B:229	BINDING SITE FOR RESIDUE HEM B 150
4	AC4	SOFTWARE	PHE B:28 , TYR B:29 , PRO B:54 , LEU B:57 , HEM B:150	BINDING SITE FOR RESIDUE IMD B 170

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

Asymmetric/Biological Unit

No.	Residues
1	Ala B:144	-	Val B:145

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

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

(no "Exon" information available for 3VHB)

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
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Chain A from PDB  Type:PROTEIN  Length:135
 aligned with BAHG_VITST | P04252 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
           BAHG_VITST     2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
               SCOP domains d3vhba_ A: Bacterial dimeric hemoglobin                                                                                                          SCOP domains
               CATH domains 3vhbA00 A:2-145 Globins                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.---------....hhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vhb A   2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLF---------QPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
                                    11        21        31        41 |       - |      61        71        81        91       101       111       121       131       141    
                                                                    43        53

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with BAHG_VITST | P04252 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
           BAHG_VITST     2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
               SCOP domains d3vhbb_ B: Bacterial dimeric hemoglobin                                                                                                          SCOP domains
               CATH domains 3vhbB00 B:2-145 Globins                                                                                                                          CATH domains
           Pfam domains (1) ----Globin-3vhbB01 B:6-103                                                                            ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----Globin-3vhbB02 B:6-103                                                                            ------------------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhh....---------..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vhb B   2 LDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLF---------QPKALAMTVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDILDAWGKAYGVIADVFIQVEADLYAQAV 145
                                    11        21        31        41 |       - |      61        71        81        91       101       111       121       131       141    
                                                                    43        53

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: Bacterial dimeric hemoglobin (4)

Vitreoscilla stercoraria [TaxId: 61] (4)

1a	d3vhba_	A:
1b	d3vhbb_	B:

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)

Vitreoscilla stercoraria. Organism_taxid: 61. Strain: c1. (4)

1a	3vhbA00	A:2-145
1b	3vhbB00	B:2-145

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Vitreoscilla stercoraria (3)

1a	Globin-3vhbB01	B:6-103
1b	Globin-3vhbB02	B:6-103

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BAHG_VITST | P04252)

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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	Cis Peptide Bonds
		Ala B:144 - Val B:145	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3VHB)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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