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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MAVICYANIN FROM CUCURBITA PEPO MEDULLOSA (ZUCCHINI)

Authors :   Y. Xie, T. Inoue, Y. Miyamoto, H. Matsumura, K. Kataoka, K. Yamaguchi, M. Nojini, S. Suzuki, Y. Kai

Date :   02 Nov 04 (Deposition) - 23 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Reduced Form, Mavicyanin, Phytocyanin, Cupredoxin, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Xie, T. Inoue, Y. Miyamoto, H. Matsumura, K. Kataoka, K. Yamaguchi, M. Nojini, S. Suzuki, Y. Kai
Structural Reorganization Of The Copper Binding Site Involving Thr15 Of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) Upon Reduction.
J. Biochem. (Tokyo) V. 137 455 2005
PubMed-ID: 15858169 | Reference-DOI: 10.1093/JB/MVI062
(for further references see the PDB file header)

Molecule 1 - MAVICYANIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	CUCURBITA PEPO
	Organism Taxid	:	3663

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CU1	4	Ligand/Ion	COPPER (I) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:45 , CYS A:86 , HIS A:91 , GLN A:96	BINDING SITE FOR RESIDUE CU1 A 1001
2	AC2	SOFTWARE	HIS B:45 , CYS B:86 , HIS B:91 , GLN B:96	BINDING SITE FOR RESIDUE CU1 B 1002
3	AC3	SOFTWARE	HIS C:45 , CYS C:86 , HIS C:91 , GLN C:96	BINDING SITE FOR RESIDUE CU1 C 1003
4	AC4	SOFTWARE	THR D:15 , HIS D:45 , CYS D:86 , HIS D:91 , GLN D:96	BINDING SITE FOR RESIDUE CU1 D 1004

Asymmetric/Biological Unit

No.	Residues
1	A:58	-	A:92
2	B:58	-	B:92
3	C:58	-	C:92
4	D:58	-	D:92

(no "Cis Peptide Bond" information available for 1WS7)

(no "SAP(SNP)/Variant" information available for 1WS7)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHYTOCYANIN	PS51485	Phytocyanin domain profile.	MAVI_CUCPE	2-103	4	A:3-104 B:3-103 C:3-103 D:3-104
2	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	MAVI_CUCPE	79-95	4	A:80-96 B:80-96 C:80-96 D:80-96

(no "Exon" information available for 1WS7)

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:107
 aligned with MAVI_CUCPE | P80728 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:107
                             1                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       
           MAVI_CUCPE     - -ATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVDPGSS 106
               SCOP domains d1ws7a_ A: Mavicyanin                                                                                       SCOP domains
               CATH domains 1ws7A00 A:1-107 Cupredoxins -  blue copper proteins                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhh.......hhhhhhhh.......eeeee.......eeeehhhhhhhh......eee...eeeee....eeeeee.....hhhhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PHYTOCYANIN  PDB: A:3-104 UniProt: 2-103                                                              --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------COPPER_BLUE      ----------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1ws7 A   1 MATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVDPGSS 107
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with MAVI_CUCPE | P80728 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:103
                             1                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99   
           MAVI_CUCPE     - -ATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVD 102
               SCOP domains d1ws7b_ B: Mavicyanin                                                                                   SCOP domains
               CATH domains 1ws7B00 B:1-103 Cupredoxins -  blue copper proteins                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhh.......hhhhhhhh.......eeeee.......eeeehhhhhhhh......eee...eeeee....eeeeee...........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PHYTOCYANIN  PDB: B:3-103 UniProt: 2-103                                                              PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1ws7 B   1 MATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVD 103
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:103
 aligned with MAVI_CUCPE | P80728 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:103
                             1                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99   
           MAVI_CUCPE     - -ATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVD 102
               SCOP domains d1ws7c_ C: Mavicyanin                                                                                   SCOP domains
               CATH domains 1ws7C00 C:1-103 Cupredoxins -  blue copper proteins                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhh.......hhhhhhhh.......eeeee.......eeeehhhhhhhh......eee...eeeee....eeeeee...........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PHYTOCYANIN  PDB: C:3-103 UniProt: 2-103                                                              PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1ws7 C   1 MATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVD 103
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:105
 aligned with MAVI_CUCPE | P80728 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:105
                             1                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99     
           MAVI_CUCPE     - -ATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVDPG 104
               SCOP domains d1ws7d_ D: Mavicyanin                                                                                     SCOP domains
               CATH domains 1ws7D00 D:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
           Pfam domains (1) ------------Cu_bind_like-1ws7D01 D:13-96                                                        --------- Pfam domains (1)
           Pfam domains (2) ------------Cu_bind_like-1ws7D02 D:13-96                                                        --------- Pfam domains (2)
           Pfam domains (3) ------------Cu_bind_like-1ws7D03 D:13-96                                                        --------- Pfam domains (3)
           Pfam domains (4) ------------Cu_bind_like-1ws7D04 D:13-96                                                        --------- Pfam domains (4)
         Sec.struct. author ...eee.hhhhh.......hhhhhhhh.......eeeee.......eeeehhhhhhhh......eee...eeeee....eeeeee.....hhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PHYTOCYANIN  PDB: D:3-104 UniProt: 2-103                                                              - PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------COPPER_BLUE      --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1ws7 D   1 MATVHKVGDSTGWTTLVPYDYAKWASSNKFHVGDSLLFNYNNKFHNVLQVDQEQFKSCNSSSPAASYTSGADSIPLKRPGTFYFLCGIPGHCQLGQKVEIKVDPG 105
                                    10        20        30        40        50        60        70        80        90       100

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 beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Mavicyanin (2)

Zucchini (Cucurbita pepo) [TaxId: 3663] (2)

1a	d1ws7a_	A:
1b	d1ws7b_	B:
1c	d1ws7c_	C:
1d	d1ws7d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Cucurbita pepo. Organism_taxid: 3663. (2)

1a	1ws7A00	A:1-107
1b	1ws7D00	D:1-105
1c	1ws7B00	B:1-103
1d	1ws7C00	C:1-103

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu_bind_like (3)

Cucurbita pepo (Vegetable marrow) (Summer squash) (2)

1a	Cu_bind_like-1ws7D01	D:13-96
1b	Cu_bind_like-1ws7D02	D:13-96
1c	Cu_bind_like-1ws7D03	D:13-96
1d	Cu_bind_like-1ws7D04	D:13-96

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (MAVI_CUCPE | P80728)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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.

Asymmetric/Biological Unit
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	1ws7
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	MAVI_CUCPE \| P80728	:	1ws8

1ws8	THE OXIDIZED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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