3QQR - 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 PARASPONIA HEMOGLOBIN; DIFFERENTIAL HEME COORDINATION IS LINKED TO QUATERNARY STRUCTURE

Authors :   S. Kakar, R. Sturms, A. Savage, J. C. Nix, A. Dispirito, M. S. Hargrove

Date :   16 Feb 11 (Deposition) - 27 Apr 11 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.16

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

Keywords :   Globin Fold, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kakar, R. Sturms, A. Tiffany, J. C. Nix, A. A. Dispirito, M. S. Hargrove
Crystal Structures Of Parasponia And Trema Hemoglobins: Differential Heme Coordination Is Linked To Quaternary Structure.
Biochemistry V. 50 4273 2011
PubMed-ID: 21491905 | Reference-DOI: 10.1021/BI2002423

Molecule 1 - NON-LEGUME HEMOGLOBIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SPONIA ANDERSONII
	Organism Scientific	:	PARASPONIA ANDERSONII
	Organism Taxid	:	3476

		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 (2, 7)

No.	Name	Count	Type	Full Name
1	DIO	5	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	DIO	4	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DIO	1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:50 , PHE A:51 , TYR A:53 , LYS A:66 , HIS A:70 , THR A:73 , ARG A:100 , ILE A:101 , ILE A:104 , HIS A:105 , VAL A:110 , HIS A:114 , PHE A:115 , THR A:118 , TYR A:146 , LEU A:149 , HOH A:178 , HOH A:189	BINDING SITE FOR RESIDUE HEM A 163
2	AC2	SOFTWARE	LEU B:50 , PHE B:51 , SER B:52 , HIS B:70 , ARG B:100 , ILE B:104 , HIS B:105 , THR B:108 , VAL B:110 , HIS B:114 , PHE B:115 , THR B:118 , LEU B:149 , ILE B:153 , HOH B:221	BINDING SITE FOR RESIDUE HEM B 163
3	AC3	SOFTWARE	LYS A:127 , TRP A:134 , LYS A:139 , HOH B:188	BINDING SITE FOR RESIDUE DIO A 164
4	AC4	SOFTWARE	ARG A:119 , LYS A:139 , ASN A:140 , HOH A:194	BINDING SITE FOR RESIDUE DIO A 165
5	AC5	SOFTWARE	LYS B:127 , TRP B:134 , LYS B:139	BINDING SITE FOR RESIDUE DIO B 164
6	AC6	SOFTWARE	PHE A:115 , GLU A:116 , ARG A:119 , TYR A:146 , ASP A:147 , VAL A:150 , LYS A:154 , HOH A:227	BINDING SITE FOR RESIDUE DIO A 166
7	AC7	SOFTWARE	GLU A:12 , GLU A:13 , ARG A:86 , HOH A:232 , SER B:52 , TYR B:53	BINDING SITE FOR RESIDUE DIO A 167

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBPL_PARAD_001 *	E	31	D	HBPL_PARAD	---	---	A/B	E	31	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBPL_PARAD_001 *	E	31	D	HBPL_PARAD	---	---	A	E	31	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBPL_PARAD_001 *	E	31	D	HBPL_PARAD	---	---	B	E	31	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBPL_PARAD	10-153	2	A:10-153 B:10-153
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBPL_PARAD	64-75	2	A:64-75 B:64-75

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBPL_PARAD	10-153	1	A:10-153 -
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBPL_PARAD	64-75	1	A:64-75 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBPL_PARAD	10-153	1	- B:10-153
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBPL_PARAD	64-75	1	- B:64-75

(no "Exon" information available for 3QQR)

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:146
 aligned with HBPL_PARAD | P68168 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:151
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           HBPL_PARAD     9 VFTEEQEALVVKAWAVMKKNSAELGLQFFLKIFEIAPSAKNLFSYLKDSPVPLEQNPKLKPHATTVFVMTCESAVQLRKAGKATVKESDLKRIGAIHFKTGVVNEHFEVTRFALLETIKEAVPEMWSPEMKNAWGVAYDQLVAAIKFEMKP 159
               SCOP domains d3qqra_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh----.-....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------D-------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLOBIN  PDB: A:10-153 UniProt: 10-153                                                                                                           ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------PLANT_GLOBIN------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qqr A   9 VFTEEQEALVVKAWAVMKKNSAELGLQFFLKIFEIAPSAKNLFSYLK----P-EQNPKLKPHATTVFVMTCESAVQLRKAGKVTVKESDLKRIGAIHFKTGVVNEHFEVTRFALLETIKEAVPEMWSPEMKNAWGVAYDQLVAAIKFEMKP 159
                                    18        28        38        48      |  - | |    68        78        88        98       108       118       128       138       148       158 
                                                                         55   60 |                                                                                                 
                                                                                62

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with HBPL_PARAD | P68168 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:151
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           HBPL_PARAD     9 VFTEEQEALVVKAWAVMKKNSAELGLQFFLKIFEIAPSAKNLFSYLKDSPVPLEQNPKLKPHATTVFVMTCESAVQLRKAGKATVKESDLKRIGAIHFKTGVVNEHFEVTRFALLETIKEAVPEMWSPEMKNAWGVAYDQLVAAIKFEMKP 159
               SCOP domains d3qqrb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Globin-3qqrB01 B:14-123                                                                                       ------------------------------------ Pfam domains (1)
           Pfam domains (2) -----Globin-3qqrB02 B:14-123                                                                                       ------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-.-.-...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------D-------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLOBIN  PDB: B:10-153 UniProt: 10-153                                                                                                           ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------PLANT_GLOBIN------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qqr B   9 VFTEEQEALVVKAWAVMKKNSAELGLQFFLKIFEIAPSAKNLFSYLK-S-V-LEQNPKLKPHATTVFVMTCESAVQLRKAGKVTVKESDLKRIGAIHFKTGVVNEHFEVTRFALLETIKEAVPEMWSPEMKNAWGVAYDQLVAAIKFEMKP 159
                                    18        28        38        48      | |-| |     68        78        88        98       108       118       128       138       148       158 
                                                                         55 | | |                                                                                                  
                                                                           57 | |                                                                                                  
                                                                             59 |                                                                                                  
                                                                               61

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: Globins (1157)

Protein domain: automated matches (99)

Parasponia andersonii [TaxId: 3476] (1)

1a	d3qqra_	A:
1b	d3qqrb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Parasponia andersonii (Sponia andersonii) (1)

1a	Globin-3qqrB01	B:14-123
1b	Globin-3qqrB02	B:14-123

Asymmetric Unit(hide GO term definitions)

Chain A,B (HBPL_PARAD | P68168)

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:0009399	nitrogen fixation	The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
	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
		DIO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

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

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
	3qqr
		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
	HBPL_PARAD \| P68168
		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
	HBPL_PARAD \| P68168
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3QQR)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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