3AQ9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRUNCATED HEMOGLOBIN FROM TETRAHYMENA PYRIFORMIS, Q50E MUTANT, FE(III) FORM

Authors :   J. Igarashi, K. Kobayashi, A. Matsuoka

Date :   25 Oct 10 (Deposition) - 20 Apr 11 (Release) - 20 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

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

Keywords :   2/2 Fold Hemoglobin, Nitric Oxide Detoxification, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Igarashi, K. Kobayashi, A. Matsuoka
A Hydrogen-Bonding Network Formed By The B10-E7-E11 Residue Of A Truncated Hemoglobin From Tetrahymena Pyriformis Is Critical For Stability Of Bound Oxygen And Nitric Oxide Detoxification.
J. Biol. Inorg. Chem. V. 16 599 2011
PubMed-ID: 21298303 | Reference-DOI: 10.1007/S00775-011-0761-3

Molecule 1 - GROUP 1 TRUNCATED HEMOGLOBIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21C(+)
	Expression System Strain	:	BL21(DE3) CODON PLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	TETRAHYMENA PYRIFORMIS
	Organism Taxid	:	5908

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:37 , PHE A:38 , THR A:41 , GLN A:46 , GLN A:49 , PHE A:53 , TYR A:64 , GLY A:66 , LYS A:67 , MET A:69 , HIS A:73 , MET A:76 , LEU A:78 , HIS A:82 , PHE A:83 , ILE A:86 , ILE A:111 , MET A:118 , HOH A:122 , HOH A:161 , HOH A:179 , HOH A:215 , HOH A:233	BINDING SITE FOR RESIDUE HEM A 144
2	AC2	SOFTWARE	PHE B:37 , PHE B:38 , THR B:41 , GLN B:46 , GLN B:49 , GLU B:50 , PHE B:53 , TYR B:64 , GLY B:66 , LYS B:67 , MET B:69 , HIS B:73 , MET B:76 , LEU B:78 , HIS B:82 , PHE B:83 , ILE B:86 , ILE B:111 , MET B:118 , HOH B:123 , HOH B:167 , HOH B:190	BINDING SITE FOR RESIDUE HEM B 144

(no "SS Bond" information available for 3AQ9)

(no "Cis Peptide Bond" information available for 3AQ9)

(no "SAP(SNP)/Variant" information available for 3AQ9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN_FAM_2	PS01213	Protozoan/cyanobacterial globins signature.	TRHBN_TETPY	53-73	2	A:53-73 B:53-73

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN_FAM_2	PS01213	Protozoan/cyanobacterial globins signature.	TRHBN_TETPY	53-73	1	A:53-73 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN_FAM_2	PS01213	Protozoan/cyanobacterial globins signature.	TRHBN_TETPY	53-73	1	- B:53-73

(no "Exon" information available for 3AQ9)

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
	(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:117
 aligned with TRHBN_TETPY | P17724 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:117
                                    14        24        34        44        54        64        74        84        94       104       114       
          TRHBN_TETPY     5 QTIYEKLGGENAMKAAVPLFYKKVLADERVKHFFKNTDMDHQTKQQTDFLTMLLGGPNHYKGKNMTEAHKGMNLQNLHFDAIIENLAATLKELGVTDAVINEAAKVIEHTRKDMLGK 121
               SCOP domains d3aq9a_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------GLOBIN_FAM_2         ------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3aq9 A   5 QTIYEKLGGENAMKAAVPLFYKKVLADERVKHFFKNTDMDHQTKQETDFLTMLLGGPNHYKGKNMTEAHKGMNLQNLHFDAIIENLAATLKELGVTDAVINEAAKVIEHTRKDMLGK 121
                                    14        24        34        44        54        64        74        84        94       104       114

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with TRHBN_TETPY | P17724 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:117
                                    14        24        34        44        54        64        74        84        94       104       114       
          TRHBN_TETPY     5 QTIYEKLGGENAMKAAVPLFYKKVLADERVKHFFKNTDMDHQTKQQTDFLTMLLGGPNHYKGKNMTEAHKGMNLQNLHFDAIIENLAATLKELGVTDAVINEAAKVIEHTRKDMLGK 121
               SCOP domains d3aq9b_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------GLOBIN_FAM_2         ------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3aq9 B   5 QTIYEKLGGENAMKAAVPLFYKKVLADERVKHFFKNTDMDHQTKQETDFLTMLLGGPNHYKGKNMTEAHKGMNLQNLHFDAIIENLAATLKELGVTDAVINEAAKVIEHTRKDMLGK 121
                                    14        24        34        44        54        64        74        84        94       104       114

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: automated matches (42)

Protein domain: automated matches (42)

Tetrahymena pyriformis [TaxId: 5908] (5)

1a	d3aq9a_	A:
1b	d3aq9b_	B:

(no "CATH Domain" information available for 3AQ9)

(no "Pfam Domain" information available for 3AQ9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRHBN_TETPY | P17724)

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 Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3aq9)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3aq9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TRHBN_TETPY \| P17724
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TRHBN_TETPY \| P17724
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TRHBN_TETPY \| P17724	:	3aq5 3aq6 3aq7 3aq8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File