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Title :   CRYSTAL STRUCTURE OF AMICYANIN SUBSTITUTED WITH COBALT

Authors :   C. J. Carrell, X. Wang, L. Jones, W. L. Jarrett, V. L. Davidson, F. S. Mathews

Date :   04 May 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Carrell, X. Wang, L. Jones, W. L. Jarrett, V. L. Davidson, F. S. Mathews
Crystallographic And Nmr Investigation Of Cobalt-Substituted Amicyanin.
Biochemistry V. 43 9381 2004
PubMed-ID: 15260481 | Reference-DOI: 10.1021/BI049635R
(for further references see the PDB file header)

Molecule 1 - AMICYANIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	MAUC, AMI
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	CO	4	Ligand/Ion	COBALT (II) ION
2	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:52 , HIS A:53 , CYS A:92 , HIS A:95 , HOH A:780	BINDING SITE FOR RESIDUE CO A 107
2	AC2	SOFTWARE	VAL A:58 , ARG A:99 , HOH A:720 , HOH A:723 , HOH A:731 , HOH A:758 , HOH A:763 , HOH A:798 , HOH A:805	BINDING SITE FOR RESIDUE PO4 A 711
3	AC3	SOFTWARE	ASP A:89 , LYS A:101 , HOH A:761 , HOH A:804	BINDING SITE FOR RESIDUE PO4 A 712
4	AC4	SOFTWARE	LYS A:27 , GLU A:49 , HOH A:744 , HOH A:835 , HOH C:858	BINDING SITE FOR RESIDUE PO4 A 713
5	AC5	SOFTWARE	HIS B:53 , CYS B:92 , HIS B:95 , HOH B:778	BINDING SITE FOR RESIDUE CO B 107
6	AC6	SOFTWARE	THR B:87 , ASP B:89 , LYS B:101 , HOH B:818 , HOH B:823 , HOH B:827 , HOH B:876 , HOH B:882	BINDING SITE FOR RESIDUE PO4 B 722
7	AC7	SOFTWARE	PRO C:52 , HIS C:53 , CYS C:92 , HIS C:95 , HOH C:751	BINDING SITE FOR RESIDUE CO C 107
8	AC8	SOFTWARE	VAL C:58 , ARG C:99 , HOH C:735 , HOH C:737 , HOH C:741 , HOH C:776 , HOH C:809 , HOH C:841 , HOH C:844	BINDING SITE FOR RESIDUE PO4 C 731
9	AC9	SOFTWARE	HIS D:53 , CYS D:92 , HIS D:95 , MET D:98 , HOH D:148	BINDING SITE FOR RESIDUE CO D 107

(no "SS Bond" information available for 1T5K)

(no "Cis Peptide Bond" information available for 1T5K)

(no "SAP(SNP)/Variant" information available for 1T5K)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	4	A:85-98 B:85-98 C:85-98 D:85-98

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	A:85-98 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	- B:85-98 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	- - C:85-98 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	- - - D:85-98

(no "Exon" information available for 1T5K)

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:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1t5ka_ A: Amicyanin                                                                                      SCOP domains
               CATH domains 1t5kA00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1t5k A   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1t5kb_ B: Amicyanin                                                                                      SCOP domains
               CATH domains 1t5kB00 B:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1t5k B   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1t5kc_ C: Amicyanin                                                                                      SCOP domains
               CATH domains 1t5kC00 C:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1t5k C   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d1t5kd_ D: Amicyanin                                                                                      SCOP domains
               CATH domains 1t5kD00 D:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
           Pfam domains (1) ----------------Copper-bind-1t5kD01 D:17-105                                                              Pfam domains (1)
           Pfam domains (2) ----------------Copper-bind-1t5kD02 D:17-105                                                              Pfam domains (2)
           Pfam domains (3) ----------------Copper-bind-1t5kD03 D:17-105                                                              Pfam domains (3)
           Pfam domains (4) ----------------Copper-bind-1t5kD04 D:17-105                                                              Pfam domains (4)
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1t5k D   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 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 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: Amicyanin (34)

Paracoccus denitrificans [TaxId: 266] (33)

1a	d1t5ka_	A:
1b	d1t5kb_	B:
1c	d1t5kc_	C:
1d	d1t5kd_	D:

Asymmetric 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)

Paracoccus denitrificans. Organism_taxid: 266. (20)

1a	1t5kA00	A:1-105
1b	1t5kB00	B:1-105
1c	1t5kC00	C:1-105
1d	1t5kD00	D:1-105

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Paracoccus denitrificans (11)

1a	Copper-bind-1t5kD01	D:17-105
1b	Copper-bind-1t5kD02	D:17-105
1c	Copper-bind-1t5kD03	D:17-105
1d	Copper-bind-1t5kD04	D:17-105

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AMCY_PARDE | P22364)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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Description

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Ligands, Modified Residues, Ions (2, 9)

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