1QJS - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   MAMMALIAN BLOOD SERUM HAEMOPEXIN GLYCOSYLATED-NATIVE PROTEIN AND IN COMPLEX WITH ITS LIGAND HAEM

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

Date :   01 Jul 99 (Deposition) - 03 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Transport Protein, Haem Binding Protein, Beta Propeller, Haem Binding And Transport, Iron Metabolism (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

Molecule 1 - HEMOPEXIN
	Chains	:	A, B
	Fragment	:	BETA-PROPELLER DOMAIN, HAEM LIGAND
	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 266
	Tissue	:	BLOOD SERUM

		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 (4, 16)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NA	8	Ligand/Ion	SODIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:284 , PHE A:285 , ALA A:336 , PHE A:337 , VAL A:338 , ALA A:379 , LEU A:380 , CYS A:381 , NA A:522	BINDING SITE FOR RESIDUE PO4 A 501
02	AC2	SOFTWARE	THR A:36 , ALA A:77 , ALA A:123 , SER A:167 , ALA A:168 , NA A:513	BINDING SITE FOR RESIDUE CL A 511
03	AC3	SOFTWARE	ASP A:34 , ASP A:75 , ASP A:121 , THR A:166	BINDING SITE FOR RESIDUE NA A 512
04	AC4	SOFTWARE	THR A:36 , ALA A:77 , ALA A:123 , ALA A:168 , CL A:511	BINDING SITE FOR RESIDUE NA A 513
05	AC5	SOFTWARE	ALA A:284 , ALA A:335 , ALA A:336 , ALA A:379 , NA A:522	BINDING SITE FOR RESIDUE CL A 521
06	AC6	SOFTWARE	MET A:239 , ALA A:284 , ALA A:336 , ALA A:379 , PO4 A:501 , CL A:521	BINDING SITE FOR RESIDUE NA A 522
07	AC7	SOFTWARE	SER A:237 , ASP A:282 , ASP A:334 , ASP A:377	BINDING SITE FOR RESIDUE NA A 523
08	AC8	SOFTWARE	ALA B:284 , PHE B:285 , ALA B:336 , PHE B:337 , VAL B:338 , ALA B:379 , LEU B:380 , CYS B:381 , NA B:522	BINDING SITE FOR RESIDUE PO4 B 501
09	AC9	SOFTWARE	ALA B:35 , THR B:36 , ALA B:77 , SER B:167 , ALA B:168 , NA B:513	BINDING SITE FOR RESIDUE CL B 511
10	BC1	SOFTWARE	ASP B:34 , ASP B:75 , ASP B:121 , THR B:166	BINDING SITE FOR RESIDUE NA B 512
11	BC2	SOFTWARE	THR B:36 , ALA B:77 , ALA B:123 , ALA B:168 , CL B:511	BINDING SITE FOR RESIDUE NA B 513
12	BC3	SOFTWARE	ALA B:284 , ALA B:335 , ALA B:336 , ALA B:379 , NA B:522	BINDING SITE FOR RESIDUE CL B 521
13	BC4	SOFTWARE	MET B:239 , ALA B:284 , ALA B:336 , ALA B:379 , PO4 B:501 , CL B:521	BINDING SITE FOR RESIDUE NA B 522
14	BC5	SOFTWARE	SER B:237 , ASP B:282 , ASP B:334 , ASP B:377	BINDING SITE FOR RESIDUE NA B 523
15	BC6	SOFTWARE	HIS A:56 , TRP A:171 , ARG A:174 , TYR A:176 , ARG A:185 , TYR A:197 , PHE A:205 , HIS A:213 , HIS A:225 , SER A:227 , HIS A:266 , PRO A:269 , HIS A:272	BINDING SITE FOR RESIDUE HEM A 500
16	BC7	SOFTWARE	HIS B:56 , TYR B:176 , PHE B:183 , TYR B:197 , LEU B:199 , TYR B:204 , PHE B:205 , HIS B:213 , ARG B:214 , HIS B:266	BINDING SITE FOR RESIDUE HEM B 500

Asymmetric Unit

No.	Residues
1	A:27	-	A:208
2	A:126	-	A:131
3	A:165	-	A:177
4	A:230	-	A:433
5	A:339	-	A:381
6	A:391	-	A:408
7	B:27	-	B:208
8	B:126	-	B:131
9	B:165	-	B:177
10	B:230	-	B:433
11	B:339	-	B:381
12	B:391	-	B:408

Asymmetric Unit

No.	Residues
1	Phe A:118	-	Pro A:119
2	Tyr A:197	-	Pro A:198
3	Tyr A:314	-	Pro A:315
4	Phe B:118	-	Pro B:119
5	Tyr B:197	-	Pro B:198
6	Tyr B:314	-	Pro B:315

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

Asymmetric Unit (2, 18)

	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	16	A:30-70 B:30-70 A:71-116 B:71-116 A:162-208 B:162-208 A:117-161 B:117-161 A:232-277 B:232-277 A:278-325 B:278-325 A:330-369 B:330-369 A:373-423 B:373-423
2	HEMOPEXIN	PS00024	Hemopexin domain signature.	HEMO_RABIT	295-310	2	A:270-285 B:270-285

Biological Unit 1 (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:232-277 - A:278-325 - A:330-369 - A:373-423 -
2	HEMOPEXIN	PS00024	Hemopexin domain signature.	HEMO_RABIT	295-310	1	A:270-285 -

Biological Unit 2 (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	- B:30-70 - B:71-116 - B:162-208 - B:117-161 - B:232-277 - B:278-325 - B:330-369 - B:373-423
2	HEMOPEXIN	PS00024	Hemopexin domain signature.	HEMO_RABIT	295-310	1	- B:270-285

(no "Exon" information available for 1QJS)

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:408
 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 d1qjsa1 A:24-218 Hemopexin                                                                                                                                                                         ----d1qjsa2 A:223-435 Hemopexin                                                                                                                                                                                           SCOP domains
               CATH domains 1qjsA01 A:24-213 Hemopexin                                                                                                                                                                    --1qj    sA02 A:216-433 Hemopexin                                                                                                                                                                                           -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......eeee.....eeeee..eeee....eeeehhhhh........eeeee...eeeeee..eeeee............hhhhh........eeeee........eeeeee..eeeeee....eeeee.........eeeee..eeeeee..eeee................hhh..............----..hhhhhhh......eeee.....eeeee..eeee.........eeehhhhh........eeeee..eeeeee..eeeeee..............hhhhhh...........eee......eeeeee..eeeeee..hhhhh..eee........eeeee..............eeeeee..eeeee.hhhhhhhh........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:232-277 UniProt: 257-302  HEMOPEXIN_2  PDB: A:278-325 UniProt: 303-350    ----HEMOPEXIN_2  PDB: A:330-369             ---HEMOPEXIN_2  PDB: A:373-423 UniProt: 398-448       ------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjs A  24 IEQCSDGWSFDATTLDDNGTMLFFKDEFVWKSHRGIRELISERWKNFIGPVDAAFRHGHTSVYLIKGDKVWVYTSEKNEKVYPKSLQDEFPGIPFPLDAAVECHRGECQDEGILFFQGNRKWFWDLTTGTKKERSWPAVGNCTSALRWLGRYYCFQGNQFLRFNPVSGEVPPGYPLDVRDYFLSCPGRGHRSSHR----HGHESTRCDPDLVLSAMVSDNHGATYVFSGSHYWRLDTNRDGWHSWPIAHQWPQGPSTVDAAFSWEDKLYLIQDTKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVCPGSSRLHIMAGRRLWWLDLKSGAQATWTELPWPHEKVDGALCMEKPLGPNSCSTSGPNLYLIHGPNLYCYRHVDKLNAAKNLPQPQRVSRLLGCTH 435
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    |  223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433  
                                                                                                                                                                                                                            218  223

Chain B from PDB  Type:PROTEIN  Length:408
 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 d1qjsb1 B:24-218 Hemopexin                                                                                                                                                                         ----d1qjsb2 B:223-435 Hemopexin                                                                                                                                                                                           SCOP domains
               CATH domains 1qjsB01 B:24-213 Hemopexin                                                                                                                                                                    --1qj    sB02 B:216-433 Hemopexin                                                                                                                                                                                           -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......eeee.....eeeee..eeee....eeeehhhhh........eeeee...eeeeee..eeeee............hhhhh........eeeee........eeeeee..eeeeee....eeeee.........eeeee..eeeeee..eeee................hhh..............----..hhhhhhh......eeee.....eeeee..eeee.........eeehhhhh........eeeee..eeeeee..eeeeee..............hhhhhh...........eee......eeeeee..eeeeee..hhhhh..eee........eeeee..............eeeeee..eeeee.hhhhhhhh........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------HEMOPEXIN_2  PDB: B:30-70 UniProt: 55-95 HEMOPEXIN_2  PDB: B:71-116 UniProt: 96-141    HEMOPEXIN_2  PDB: B:117-161 UniProt: 142-186 HEMOPEXIN_2  PDB: B:162-208 UniProt: 187-233   -----------------------HEMOPEXIN_2  PDB: B:232-277 UniProt: 257-302  HEMOPEXIN_2  PDB: B:278-325 UniProt: 303-350    ----HEMOPEXIN_2  PDB: B:330-369             ---HEMOPEXIN_2  PDB: B:373-423 UniProt: 398-448       ------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjs B  24 IEQCSDGWSFDATTLDDNGTMLFFKDEFVWKSHRGIRELISERWKNFIGPVDAAFRHGHTSVYLIKGDKVWVYTSEKNEKVYPKSLQDEFPGIPFPLDAAVECHRGECQDEGILFFQGNRKWFWDLTTGTKKERSWPAVGNCTSALRWLGRYYCFQGNQFLRFNPVSGEVPPGYPLDVRDYFLSCPGRGHRSSHR----HGHESTRCDPDLVLSAMVSDNHGATYVFSGSHYWRLDTNRDGWHSWPIAHQWPQGPSTVDAAFSWEDKLYLIQDTKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVCPGSSRLHIMAGRRLWWLDLKSGAQATWTELPWPHEKVDGALCMEKPLGPNSCSTSGPNLYLIHGPNLYCYRHVDKLNAAKNLPQPQRVSRLLGCTH 435
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    |  223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433  
                                                                                                                                                                                                                            218  223

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	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 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	d1qjsa1	A:24-218
1b	d1qjsa2	A:223-435
1c	d1qjsb1	B:24-218
1d	d1qjsb2	B:223-435

Asymmetric 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	1qjsA02	A:216-433
1b	1qjsB02	B:216-433
1c	1qjsA01	A:24-213
1d	1qjsB01	B:24-213

(no "Pfam Domain" information available for 1QJS)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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	Cis Peptide Bonds
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		Phe B:118 - Pro B:119	[ RasMol ]
		Tyr A:197 - Pro A:198	[ RasMol ]
		Tyr A:314 - Pro A:315	[ RasMol ]
		Tyr B:197 - Pro B:198	[ RasMol ]
		Tyr B:314 - Pro B:315	[ RasMol ]

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	1qjs
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	HEMO_RABIT \| P20058	:	1hxn 1qhu 4rt6

Description

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Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (12, 12)

Cis Peptide Bonds (6, 6)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File