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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM TREMA TOMENTOSA

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 :   1.84

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

Keywords :   Globin Fold, Hexacoordination, Heme Binding, Oxygen Binding, Metal Binding Protein (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-SYMBIOTIC HEMOGLOBIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLB1
	Organism Common	:	POISON PEACH
	Organism Scientific	:	TREMA TOMENTOSA
	Organism Taxid	:	3480
	Synonym	:	TRETO GLB1

		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	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:50 , PHE A:51 , HIS A:70 , LEU A:101 , HIS A:105 , ASN A:108 , HIS A:114 , PHE A:115 , THR A:118 , TYR A:146 , LEU A:149 , HOH A:174 , HOH A:188 , HOH A:257 , LYS B:107	BINDING SITE FOR RESIDUE HEM A 163
2	AC2	SOFTWARE	LEU B:50 , PHE B:51 , TYR B:53 , HIS B:70 , THR B:73 , ARG B:100 , LEU B:101 , HIS B:105 , HIS B:114 , PHE B:115 , THR B:118 , TYR B:146 , LEU B:149	BINDING SITE FOR RESIDUE HEM B 163
3	AC3	SOFTWARE	LYS B:127 , TRP B:134 , LYS B:139 , HOH B:259	BINDING SITE FOR RESIDUE SO4 B 164
4	AC4	SOFTWARE	TRP A:134 , LYS A:139 , HOH A:255	BINDING SITE FOR RESIDUE SO4 A 164

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

Asymmetric/Biological Unit

No.	Residues
1	Ile A:59	-	Pro A:60

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBL_TRETO	10-157	2	A:10-158 B:10-158
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBL_TRETO	64-75	2	A:64-75 B:64-75

(no "Exon" information available for 3QQQ)

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:150
 aligned with HBL_TRETO | P07803 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:151
                                                                                                                                       117                                         
                                                                                                                                     116 |                                         
                                    18        28        38        48        58        68        78        88        98       108       117       127       137       147       157 
            HBL_TRETO     9 VFTEEQEALVVKSWAVMKKNSAELGLKFFLKIFEIAPSAKNLFSYLKDSPIPLEQNPKLKPHAMTVFVMTCESAVQLRKAGKVTVRESNLKRLGAIHFKNGVVNEHFE-TRFALLETIKEAVPEMWSPEMKNAWGEAYDQLVAAIKSEMKP 158
               SCOP domains d3qqqa_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh-...hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLOBIN  PDB: A:10-158 UniProt: 10-157                                                                                                                - PROSITE (1)
                PROSITE (2) -------------------------------------------------------PLANT_GLOBIN------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qqq A   9 VFTEEQEALVVKSWAVMKKNSAELGLKFFLKIFEIAPSAKNLFSYLK-SPIPLEQNPKLKPHAMTVFVMTCESAVQLRKAGKVTVRESNLKRLGAIHFKNGVVNEHFEVTRFALLETIKEAVPEMWSPEMKNAWGEAYDQLVAAIKSEMKP 159
                                    18        28        38        48      | 58        68        78        88        98       108       118       128       138       148       158 
                                                                         55 |                                                                                                      
                                                                           57

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with HBL_TRETO | P07803 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:151
                                                                                                                                       117                                         
                                                                                                                                     116 |                                         
                                    18        28        38        48        58        68        78        88        98       108       117       127       137       147       157 
            HBL_TRETO     9 VFTEEQEALVVKSWAVMKKNSAELGLKFFLKIFEIAPSAKNLFSYLKDSPIPLEQNPKLKPHAMTVFVMTCESAVQLRKAGKVTVRESNLKRLGAIHFKNGVVNEHFE-TRFALLETIKEAVPEMWSPEMKNAWGEAYDQLVAAIKSEMKP 158
               SCOP domains d3qqqb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Globin-3qqqB01 B:14-124                                                                                        ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-3qqqB02 B:14-124                                                                                        ----------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....--..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLOBIN  PDB: B:10-158 UniProt: 10-157                                                                                                                - PROSITE (1)
                PROSITE (2) -------------------------------------------------------PLANT_GLOBIN------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qqq B   9 VFTEEQEALVVKSWAVMKKNSAELGLKFFLKIFEIAPSAKNLFSYLK--PIPLEQNPKLKPHAMTVFVMTCESAVQLRKAGKVTVRESNLKRLGAIHFKNGVVNEHFEVTRFALLETIKEAVPEMWSPEMKNAWGEAYDQLVAAIKSEMKP 159
                                    18        28        38        48      | 58        68        78        88        98       108       118       128       138       148       158 
                                                                         55 58

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: automated matches (99)

Trema tomentosa [TaxId: 3480] (1)

1a	d3qqqa_	A:
1b	d3qqqb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Trema tomentosa (Poison peach) (Celtis tomentosa) (1)

1a	Globin-3qqqB01	B:14-124
1b	Globin-3qqqB02	B:14-124

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HBL_TRETO | P07803)


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).

Asymmetric/Biological Unit
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		Ile A:59 - Pro A:60	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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