1QHU - JenaLib

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Title :   MAMMALIAN BLOOD SERUM HAEMOPEXIN DEGLYCOSYLATED AND IN COMPLEX WITH ITS LIGAND HAEM

Authors :   M. Paoli, H. M. Baker, W. T. Morgan, A. Smith, E. N. Baker

Date :   27 May 99 (Deposition) - 06 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Beta Propeller, Haem Binding And Transport, Iron Metabolism, Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Paoli, B. F. Anderson, H. M. Baker, W. T. Morgan, A. Smith, E. N. Baker
Crystal Structure Of Hemopexin Reveals A Novel High-Affinity Heme Site Formed Between Two Beta-Propeller Domains.
Nat. Struct. Biol. V. 6 926 1999
PubMed-ID: 10504726 | Reference-DOI: 10.1038/13294
(for further references see the PDB file header)

Molecule 1 - PROTEIN (HEMOPEXIN)
	Chains	:	A
	Fragment	:	BETA-PROPELLER DOMAIN
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Other Details	:	COVALENT LINK BETWEEN FE OF HAEM LIGAND AND I) NE2 OF HIS 213 AND II) NE2 OF HIS 265
	Tissue	:	BLOOD SERUM

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NA	4	Ligand/Ion	SODIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:36 , ALA A:77 , ALA A:123 , SER A:167 , ALA A:168 , NA A:437	BINDING SITE FOR RESIDUE CL A 435
2	AC2	SOFTWARE	ASP A:34 , ASP A:75 , ASP A:121 , THR A:166 , HOH A:526	BINDING SITE FOR RESIDUE NA A 436
3	AC3	SOFTWARE	THR A:36 , ALA A:77 , ALA A:123 , ALA A:168 , CL A:435 , HOH A:502	BINDING SITE FOR RESIDUE NA A 437
4	AC4	SOFTWARE	MET A:238 , ALA A:283 , ALA A:335 , ALA A:378 , CL A:439 , PO4 A:441	BINDING SITE FOR RESIDUE NA A 438
5	AC5	SOFTWARE	MET A:238 , ALA A:282 , ALA A:283 , ALA A:334 , ALA A:335 , ALA A:378 , NA A:438	BINDING SITE FOR RESIDUE CL A 439
6	AC6	SOFTWARE	SER A:236 , ASP A:281 , ASP A:333 , ASP A:376 , HOH A:619	BINDING SITE FOR RESIDUE NA A 440
7	AC7	SOFTWARE	ALA A:283 , PHE A:284 , ALA A:335 , PHE A:336 , VAL A:337 , ALA A:378 , LEU A:379 , CYS A:380 , NA A:438	BINDING SITE FOR RESIDUE PO4 A 441
8	AC8	SOFTWARE	TRP A:171 , ARG A:174 , TYR A:176 , PHE A:183 , ARG A:185 , TYR A:197 , TYR A:204 , PHE A:205 , HIS A:213 , ARG A:214 , HIS A:222 , GLU A:225 , HIS A:265 , TRP A:267 , PRO A:268 , HIS A:271 , HOH A:584 , HOH A:643	BINDING SITE FOR RESIDUE HEM A 500
9	HIS	AUTHOR	HIS A:213 , HIS A:265	AXIAL HAEM LIGANDS

Asymmetric/Biological Unit

No.	Residues
1	A:27	-	A:208
2	A:126	-	A:131
3	A:165	-	A:177
4	A:229	-	A:432
5	A:338	-	A:380
6	A:390	-	A:407

Asymmetric/Biological Unit

No.	Residues
1	Phe A:118	-	Pro A:119
2	Tyr A:197	-	Pro A:198
3	Tyr A:313	-	Pro A:314

(no "SAP(SNP)/Variant" information available for 1QHU)

Asymmetric/Biological Unit (2, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	HEMO_RABIT	55-95 96-141 187-233 142-186 257-302 303-350 355-394 398-448	8	A:30-70 A:71-116 A:162-208 A:117-161 A:231-276 A:277-324 A:329-368 A:372-422
2	HEMOPEXIN	PS00024	Hemopexin domain signature.	HEMO_RABIT	295-310	1	A:269-284

(no "Exon" information available for 1QHU)

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:398
 aligned with HEMO_RABIT | P20058 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:412
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458  
           HEMO_RABIT    49 IEQCSDGWSFDATTLDDNGTMLFFKDEFVWKSHRGIRELISERWKNFIGPVDAAFRHGHTSVYLIKGDKVWVYTSEKNEKVYPKSLQDEFPGIPFPLDAAVECHRGECQDEGILFFQGNRKWFWDLTTGTKKERSWPAVGNCTSALRWLGRYYCFQGNQFLRFNPVSGEVPPGYPLDVRDYFLSCPGRGHRSSHRNSTQHGHESTRCDPDLVLSAMVSDNHGATYVFSGSHYWRLDTNRDGWHSWPIAHQWPQGPSTVDAAFSWEDKLYLIQDTKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVCPGSSRLHIMAGRRLWWLDLKSGAQATWTELPWPHEKVDGALCMEKPLGPNSCSTSGPNLYLIHGPNLYCYRHVDKLNAAKNLPQPQRVSRLLGCTH 460
               SCOP domains d1qhua1 A:24-215 Hemopexin                                                                                                                                                                             d1qhua2 A:222-434 Hemopexin                                                                                                                                                                                           SCOP domains
               CATH domains 1qhuA01 A:24-213 Hemopexin                                                                                                                                                                    --       1qhuA02 A:222-433 Hemopexin                                                                                                                                                                                         - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1qhuA01 A:280-321               ----------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1qhuA02 A:280-321               ----------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1qhuA03 A:280-321               ----------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1qhuA04 A:280-321               ----------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .hhh.......eeee.....eeeee..eeee....eeeehhhh.........eeeee...eeeeee..eeeee..-------...hhhh.........eeeee........eeeeee..eeeeee....eeeee.........eeeee..eeeeee..eeeee..............hhhh...........-------...............eeee.....eeeee..eeee...hhh......hhhh.........eeeee..eeeeee..eeeeee..............hhhhh............eee......eeeeee..eeeeeehhhhhh..............eeeee..............eeeeee..eeeee..hhhhhh.........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------HEMOPEXIN_2  PDB: A:30-70 UniProt: 55-95 HEMOPEXIN_2  PDB: A:71-116 UniProt: 96-141    HEMOPEXIN_2  PDB: A:117-161 UniProt: 142-186 HEMOPEXIN_2  PDB: A:162-208 UniProt: 187-233   -----------------------HEMOPEXIN_2  PDB: A:231-276 UniProt: 257-302  HEMOPEXIN_2  PDB: A:277-324 UniProt: 303-350    ----HEMOPEXIN_2  PDB: A:329-368             ---HEMOPEXIN_2  PDB: A:372-422 UniProt: 398-448       ------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qhu A  24 IEQCSDGWSFDATTLDDNGTMLFFKDEFVWKSHRGIRELISERWKNFIGPVDAAFRHGHTSVYLIKGDKVWVYTS-------PKSLQDEFPGIPFPLDAAVECHRGECQDEGILFFQGNRKWFWDLTTGTKKERSWPAVGNCTSALRWLGRYYCFQGNQFLRFNPVSGEVPPGYPLDVRDYFLSCPGRGHRS-------HGHESTRCDPDLVLSAMVSDNHGATYVFSGSHYWRLDTNRDGWHSWPIAHQWPQGPSTVDAAFSWEDKLYLIQDTKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVCPGSSRLHIMAGRRLWWLDLKSGAQATWTELPWPHEKVDGALCMEKPLGPNSCSTSGPNLYLIHGPNLYCYRHVDKLNAAKNLPQPQRVSRLLGCTH 434
                                    33        43        53        63        73        83        93    |    -  |    113       123       133       143       153       163       173       183       193       203       213 |     222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432  
                                                                                                     98     106                                                                                                          215     222

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 4-bladed beta-propeller (15)

Superfamily: Hemopexin-like domain (15)

Family: Hemopexin-like domain (12)

Protein domain: Hemopexin (3)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (3)

1a	d1qhua1	A:24-215
1b	d1qhua2	A:222-434

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 4 Propellor (14)

Topology: Hemopexin (14)

Homologous Superfamily: Hemopexin (14)

Rabbit (Oryctolagus cuniculus) (3)

1a	1qhuA02	A:222-433
1b	1qhuA01	A:24-213

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Hemopexin] (5)

Family: Hemopexin (5)

Oryctolagus cuniculus (Rabbit) (1)

1a	Hemopexin-1qhuA01	A:280-321
1b	Hemopexin-1qhuA02	A:280-321
1c	Hemopexin-1qhuA03	A:280-321
1d	Hemopexin-1qhuA04	A:280-321

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HEMO_RABIT | P20058)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0015232	heme transporter activity	Enables the directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0015886	heme transport	The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, 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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (9, 9)

SS Bonds (6, 6)

Cis Peptide Bonds (3, 3)

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