1JS8 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A FUNCTIONAL UNIT FROM OCTOPUS HEMOCYANIN

Authors :   M. E. Cuff, K. I. Miller, K. E. Van Holde, W. A. Hendrickson

Date :   16 Aug 01 (Deposition) - 03 Oct 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Glycoprotein, Mollusc, Oxygen-Transport, Thioether Bond, Oxygen Storage-Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Cuff, K. I. Miller, K. E. Van Holde, W. A. Hendrickson
Crystal Structure Of A Functional Unit From Octopus Hemocyanin.
J. Mol. Biol. V. 278 855 1998
PubMed-ID: 9614947 | Reference-DOI: 10.1006/JMBI.1998.1647

Molecule 1 - HEMOCYANIN
	Chains	:	A, B
	Fragment	:	C-TERMINAL FUNCTIONAL UNIT, ODG
	Organism Scientific	:	OCTOPUS DOFLEINI
	Organism Taxid	:	6644
	Other Details	:	C-TERMINAL PROTEOLYTIC FRAGMENT FROM 350KDA POLYPEPTIDE SUBUNIT. NATIVE MULTIMER IS 10 SUBUNITS EXHIBITING D5 SYMMETRY.
	Strain	:	G-TYPE SEQUENCE
	Synonym	:	HEMOCYANIN G-TYPE

		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 (5, 15)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	CUO	2	Ligand/Ion	CU2-O2 CLUSTER
3	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (5, 9)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CUO	1	Ligand/Ion	CU2-O2 CLUSTER
3	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CUO	1	Ligand/Ion	CU2-O2 CLUSTER
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:538 , NAG A:891 , ASN A:2553 , THR A:2555 , HIS A:2763	BINDING SITE FOR RESIDUE NDG A 890
02	AC2	SOFTWARE	HOH A:416 , HOH A:598 , HOH A:638 , NDG A:890 , BMA A:892 , TYR A:2551	BINDING SITE FOR RESIDUE NAG A 891
03	AC3	SOFTWARE	NAG A:891 , MAN A:893 , BMA A:896	BINDING SITE FOR RESIDUE BMA A 892
04	AC4	SOFTWARE	HOH A:564 , BMA A:892 , MAN A:894 , MAN A:895 , ILE A:2804 , GLY A:2805 , TYR A:2881	BINDING SITE FOR RESIDUE MAN A 893
05	AC5	SOFTWARE	MAN A:893 , ARG A:2802 , THR A:2803 , PHE A:2837	BINDING SITE FOR RESIDUE MAN A 894
06	AC6	SOFTWARE	HOH A:570 , MAN A:893 , GLU A:2833	BINDING SITE FOR RESIDUE MAN A 895
07	AC7	SOFTWARE	BMA A:892	BINDING SITE FOR RESIDUE BMA A 896
08	AC8	SOFTWARE	NAG B:991 , ASN B:2553 , THR B:2555	BINDING SITE FOR RESIDUE NAG B 990
09	AC9	SOFTWARE	MAN A:992 , NAG B:990	BINDING SITE FOR RESIDUE NAG B 991
10	BC1	SOFTWARE	LYS A:2880 , HOH B:695 , NAG B:991 , MAN B:994 , PHE B:2837	BINDING SITE FOR RESIDUE MAN A 992
11	BC2	SOFTWARE	HOH B:548 , MAN B:994 , BMA B:995 , ILE B:2804 , GLY B:2805 , TYR B:2881	BINDING SITE FOR RESIDUE MAN B 993
12	BC3	SOFTWARE	MAN A:992 , MAN B:993 , ARG B:2802 , THR B:2803 , PHE B:2837	BINDING SITE FOR RESIDUE MAN B 994
13	BC4	SOFTWARE	MAN B:993 , GLN B:2806 , GLU B:2833	BINDING SITE FOR RESIDUE BMA B 995
14	BC5	SOFTWARE	HIS A:2543 , HIS A:2562 , PHE A:2567 , HIS A:2571 , HIS A:2671 , HIS A:2675 , HIS A:2702 , LEU A:2830	BINDING SITE FOR RESIDUE CUO A 888
15	BC6	SOFTWARE	HIS B:2543 , HIS B:2562 , PHE B:2567 , HIS B:2571 , HIS B:2671 , HIS B:2675 , HIS B:2702 , LEU B:2830	BINDING SITE FOR RESIDUE CUO B 999

Asymmetric Unit

No.	Residues
1	A:2549	-	A:2559
2	A:2661	-	A:2728
3	A:2815	-	A:2821
4	B:2549	-	B:2559
5	B:2661	-	B:2728
6	B:2815	-	B:2821

Asymmetric Unit

No.	Residues
1	Ile A:2545	-	Pro A:2546
2	Lys A:2738	-	Pro A:2739
3	Ile B:2545	-	Pro B:2546
4	Lys B:2738	-	Pro B:2739

(no "SAP(SNP)/Variant" information available for 1JS8)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYROSINASE_1	PS00497	Tyrosinase CuA-binding region signature.	HCYG_ENTDO	60-77 480-497 894-912 1312-1329 1728-1745 2144-2161 2562-2579	2	- - - - - - A:2562-2579 B:2562-2579
2	TYROSINASE_2	PS00498	Tyrosinase and hemocyanins CuB-binding region signature.	HCYG_ENTDO	625-636 1037-1048 1449-1460 1873-1884 2286-2297 2695-2706	2	- - - - - A:2695-2706 B:2695-2706

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYROSINASE_1	PS00497	Tyrosinase CuA-binding region signature.	HCYG_ENTDO	60-77 480-497 894-912 1312-1329 1728-1745 2144-2161 2562-2579	1	- - - - - - A:2562-2579 -
2	TYROSINASE_2	PS00498	Tyrosinase and hemocyanins CuB-binding region signature.	HCYG_ENTDO	625-636 1037-1048 1449-1460 1873-1884 2286-2297 2695-2706	1	- - - - - A:2695-2706 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYROSINASE_1	PS00497	Tyrosinase CuA-binding region signature.	HCYG_ENTDO	60-77 480-497 894-912 1312-1329 1728-1745 2144-2161 2562-2579	1	- - - - - - - B:2562-2579
2	TYROSINASE_2	PS00498	Tyrosinase and hemocyanins CuB-binding region signature.	HCYG_ENTDO	625-636 1037-1048 1449-1460 1873-1884 2286-2297 2695-2706	1	- - - - - - B:2695-2706

(no "Exon" information available for 1JS8)

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:382
 aligned with HCYG_ENTDO | O61363 from UniProtKB/Swiss-Prot  Length:2896

    Alignment length:390
                                  2512      2522      2532      2542      2552      2562      2572      2582      2592      2602      2612      2622      2632      2642      2652      2662      2672      2682      2692      2702      2712      2722      2732      2742      2752      2762      2772      2782      2792      2802      2812      2822      2832      2842      2852      2862      2872      2882      2892
          HCYG_ENTDO   2503 AIIRKNVNSLTPSDIKELRDAMAKVQADTSDNGYQKIASYHGIPLSCHYENGTAYACCQHGMVTFPNWHRLLTKQMEDALVAKGSHVGIPYWDWTTTFANLPVLVTEEKDNSFHHAHIDVANTDTTRSPRAQLFDDPDKGDKSFFYRQIALALEQTDFCDFEIQFEIGHNAIHSWVGGSSPYGMSTLHYTSYDPLFYLHHSNTDRIWSVWQALQKYRGLPYNTANCEINKLVKPLKPFNLDTNPNAVTKAHSTGATSFDYHKLGYDYDNLNFHGMTIPELEEHLKEIQHEDRVFAGFLLRTIGQSADVNFDVCTKDGECTFGGTFCILGGEHEMFWAFDRPFKYDITTSLKHLRLDAHDDFDIKVTIKGIDGHVLSNKYLSPPTVFLAPA 2892
               SCOP domains d1js8a1 A:2503-2791 Mollusc hemocyanin                                                                                                                                                                                                                                                           d1js8a2 A:2792-2892 C-terminal domain of mollusc hemocyanin                                           SCOP domains
               CATH domains 1js8A01 A:2503-2786 Di-copper center containing domain from catechol oxidase                                                                                                                                                                                                                1js8A02 A:2787-2892  [code=2.60.310.10, no name defined]                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.......ee.....ee........hhhhhhhhhhhhhhhhhhhh..................hhhhhh.........ee....ee.....hhhhh--------hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh...........hhhhhhh.hhhhh.hhhhh.eee...hhhhhhhhhhhhhhhhhh...eeeeee........eeeeeeeee....eeeeeeeee..............eeeehhhhhhhh.......eeeeeeeee....eehhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------TYROSINASE_1      -------------------------------------------------------------------------------------------------------------------TYROSINASE_2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1js8 A 2503 AIIRKNVNSLTPSDIKELRDAMAKVQADTSDNGYQKIASYHGIPLSCHYENGTAYACCQHGMVTFPNWHRLLTKQMEDALVAKGSHVGIPYWDWTTTFANLPVLVTEEKDNSFHHAHIDVANTDTTRSPRAQLF--------SFFYRQIALALEQTDFCDFEIQFEIGHNAIHSWVGGSSPYGMSTLHYTSYDPLFYLHHSNTDRIWSVWQALQKYRGLPYNTANCEINKLVKPLKPFNLDTNPNAVTKAHSTGATSFDYHKLGYDYDNLNFHGMTIPELEEHLKEIQHEDRVFAGFLLRTIGQSADVNFDVCTKDGECTFGGTFCILGGEHEMFWAFDRLFKYDITTSLKHLRLDAHDDFDIKVTIKGIDGHVLSNKYLSPPTVFLAPA 2892
                                  2512      2522      2532      2542      2552      2562      2572      2582      2592      2602      2612      2622      2632   |     -  |   2652      2662      2672      2682      2692      2702      2712      2722      2732      2742      2752      2762      2772      2782      2792      2802      2812      2822      2832      2842      2852      2862      2872      2882      2892
                                                                                                                                                              2636     2645

Chain B from PDB  Type:PROTEIN  Length:382
 aligned with HCYG_ENTDO | O61363 from UniProtKB/Swiss-Prot  Length:2896

    Alignment length:390
                                  2512      2522      2532      2542      2552      2562      2572      2582      2592      2602      2612      2622      2632      2642      2652      2662      2672      2682      2692      2702      2712      2722      2732      2742      2752      2762      2772      2782      2792      2802      2812      2822      2832      2842      2852      2862      2872      2882      2892
          HCYG_ENTDO   2503 AIIRKNVNSLTPSDIKELRDAMAKVQADTSDNGYQKIASYHGIPLSCHYENGTAYACCQHGMVTFPNWHRLLTKQMEDALVAKGSHVGIPYWDWTTTFANLPVLVTEEKDNSFHHAHIDVANTDTTRSPRAQLFDDPDKGDKSFFYRQIALALEQTDFCDFEIQFEIGHNAIHSWVGGSSPYGMSTLHYTSYDPLFYLHHSNTDRIWSVWQALQKYRGLPYNTANCEINKLVKPLKPFNLDTNPNAVTKAHSTGATSFDYHKLGYDYDNLNFHGMTIPELEEHLKEIQHEDRVFAGFLLRTIGQSADVNFDVCTKDGECTFGGTFCILGGEHEMFWAFDRPFKYDITTSLKHLRLDAHDDFDIKVTIKGIDGHVLSNKYLSPPTVFLAPA 2892
               SCOP domains d1js8b1 B:2503-2791 Mollusc hemocyanin                                                                                                                                                                                                                                                           d1js8b2 B:2792-2892 C-terminal domain of mollusc hemocyanin                                           SCOP domains
               CATH domains 1js8B01 B:2503-2786 Di-copper center containing domain from catechol oxidase                                                                                                                                                                                                                1js8B02 B:2787-2891  [code=2.60.310.10, no name defined]                                                 - CATH domains
           Pfam domains (1) ------------------------------Tyrosinase-1js8B01 B:2533-2715                                                                                                                                                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------Tyrosinase-1js8B02 B:2533-2715                                                                                                                                                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.......ee.....ee........hhhhhhhhhhhhhhhhhhhh..................hhhhhh.........ee....ee.....hhhhh--------hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhh.hhhhh.eee...hhhhhhhhhhhhhhhhhh...eeeeee........eeeeeeeee....eeeeeeeee..............eeeehhhhhhhhh......eeeeeeeee....ee........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------TYROSINASE_1      -------------------------------------------------------------------------------------------------------------------TYROSINASE_2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1js8 B 2503 AIIRKNVNSLTPSDIKELRDAMAKVQADTSDNGYQKIASYHGIPLSCHYENGTAYACCQHGMVTFPNWHRLLTKQMEDALVAKGSHVGIPYWDWTTTFANLPVLVTEEKDNSFHHAHIDVANTDTTRSPRAQLF--------SFFYRQIALALEQTDFCDFEIQFEIGHNAIHSWVGGSSPYGMSTLHYTSYDPLFYLHHSNTDRIWSVWQALQKYRGLPYNTANCEINKLVKPLKPFNLDTNPNAVTKAHSTGATSFDYHKLGYDYDNLNFHGMTIPELEEHLKEIQHEDRVFAGFLLRTIGQSADVNFDVCTKDGECTFGGTFCILGGEHEMFWAFDRLFKYDITTSLKHLRLDAHDDFDIKVTIKGIDGHVLSNKYLSPPTVFLAPA 2892
                                  2512      2522      2532      2542      2552      2562      2572      2582      2592      2602      2612      2622      2632   |     -  |   2652      2662      2672      2682      2692      2702      2712      2722      2732      2742      2752      2762      2772      2782      2792      2802      2812      2822      2832      2842      2852      2862      2872      2882      2892
                                                                                                                                                              2636     2645

Legend:		→ Mismatch	(orange background)
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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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Di-copper (13)

Family: Tyrosinase (10)

Enteroctopus dofleini (Giant octopus) (Octopus dofleini) (1)

1a	Tyrosinase-1js8B01	B:2533-2715
1b	Tyrosinase-1js8B02	B:2533-2715

Asymmetric Unit(hide GO term definitions)

Chain A,B (HCYG_ENTDO | O61363)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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
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	Cis Peptide Bonds
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		Ile B:2545 - Pro B:2546	[ RasMol ]
		Lys A:2738 - Pro A:2739	[ RasMol ]
		Lys B:2738 - Pro B:2739	[ RasMol ]

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	1js8
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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