1QL4 - JenaLib

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Title :   STRUCTURE OF THE SOLUBLE DOMAIN OF CYTOCHROME C552 FROM PARACOCCUS DENITRIFICANS IN THE OXIDISED STATE

Authors :   A. Harrenga, B. Reincke, H. Rueterjans, B. Ludwig, H. Michel

Date :   20 Aug 99 (Deposition) - 03 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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 Protein (Cytochrome), Electron Transfer, Oxidised (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Harrenga, B. Reincke, H. Rueterjans, B. Ludwig, H. Michel
Structure Of The Soluble Domain Of Cytochrome C552 From Paracoccus Denitrificans In The Oxidized And Reduced States
J. Mol. Biol. V. 295 667 2000
PubMed-ID: 10623555 | Reference-DOI: 10.1006/JMBI.1999.3382

Molecule 1 - CYTOCHROME C552
	Cellular Location	:	MEMBRANE-BOUND
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SOLUBLE DOMAIN
	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 (1, 4)

No.	Name	Count	Type	Full Name
1	HEC	4	Ligand/Ion	HEME C

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:13 , CYS A:14 , CYS A:17 , HIS A:18 , VAL A:26 , ARG A:36 , ALA A:39 , TYR A:46 , SER A:47 , MET A:50 , TRP A:57 , LEU A:62 , PHE A:65 , LEU A:66 , THR A:76 , LYS A:77 , MET A:78 , ALA A:79 , PHE A:80 , HOH A:2086	BINDING SITE FOR RESIDUE HEC A 101
2	AC2	SOFTWARE	LYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , VAL B:26 , PRO B:28 , ARG B:36 , ALA B:39 , TYR B:46 , SER B:47 , MET B:50 , TRP B:57 , LEU B:62 , LEU B:66 , THR B:76 , LYS B:77 , MET B:78 , HOH B:2086	BINDING SITE FOR RESIDUE HEC B 101
3	AC3	SOFTWARE	LYS C:13 , CYS C:14 , CYS C:17 , HIS C:18 , VAL C:26 , PRO C:28 , LEU C:30 , ARG C:36 , ALA C:39 , VAL C:41 , TYR C:46 , SER C:47 , MET C:50 , TRP C:57 , LEU C:62 , LEU C:66 , THR C:76 , LYS C:77 , MET C:78 , ALA C:79 , PHE C:80 , LEU C:92 , HOH C:2057 , LEU D:20	BINDING SITE FOR RESIDUE HEC C 101
4	AC4	SOFTWARE	ASN C:23 , LYS D:13 , CYS D:14 , CYS D:17 , HIS D:18 , VAL D:26 , PRO D:28 , ARG D:36 , ALA D:39 , TYR D:46 , SER D:47 , TRP D:57 , LEU D:66 , THR D:76 , LYS D:77 , MET D:78 , HOH D:2091	BINDING SITE FOR RESIDUE HEC D 101

(no "SS Bond" information available for 1QL4)

(no "Cis Peptide Bond" information available for 1QL4)

(no "SAP(SNP)/Variant" information available for 1QL4)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CY552_PARDE	78-176	4	A:2-100 B:2-100 C:2-100 D:2-100

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CY552_PARDE	78-176	1	A:2-100 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CY552_PARDE	78-176	1	- B:2-100 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CY552_PARDE	78-176	1	- - C:2-100 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CY552_PARDE	78-176	1	- - - D:2-100

(no "Exon" information available for 1QL4)

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:99
 aligned with CY552_PARDE | P54820 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:99
                                    87        97       107       117       127       137       147       157       167         
          CY552_PARDE    78 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 176
               SCOP domains d1ql4a_ A: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql4A00 A:2-100 Cytochrome c                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:2-100 UniProt: 78-176                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1ql4 A   2 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 100
                                    11        21        31        41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with CY552_PARDE | P54820 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:99
                                    87        97       107       117       127       137       147       157       167         
          CY552_PARDE    78 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 176
               SCOP domains d1ql4b_ B: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql4B00 B:2-100 Cytochrome c                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:2-100 UniProt: 78-176                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1ql4 B   2 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 100
                                    11        21        31        41        51        61        71        81        91

Chain C from PDB  Type:PROTEIN  Length:99
 aligned with CY552_PARDE | P54820 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:99
                                    87        97       107       117       127       137       147       157       167         
          CY552_PARDE    78 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 176
               SCOP domains d1ql4c_ C: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql4C00 C:2-100 Cytochrome c                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh................................hhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: C:2-100 UniProt: 78-176                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1ql4 C   2 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 100
                                    11        21        31        41        51        61        71        81        91

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with CY552_PARDE | P54820 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:99
                                    87        97       107       117       127       137       147       157       167         
          CY552_PARDE    78 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 176
               SCOP domains d1ql4d_ D: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql4D00 D:2-100 Cytochrome c                                                                        CATH domains
           Pfam domains (1) --Cytochrom_C-1ql4D01 D:4-100                                                                       Pfam domains (1)
           Pfam domains (2) --Cytochrom_C-1ql4D02 D:4-100                                                                       Pfam domains (2)
           Pfam domains (3) --Cytochrom_C-1ql4D03 D:4-100                                                                       Pfam domains (3)
           Pfam domains (4) --Cytochrom_C-1ql4D04 D:4-100                                                                       Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhh................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: D:2-100 UniProt: 78-176                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1ql4 D   2 ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 100
                                    11        21        31        41        51        61        71        81        91

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 alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: Cytochrome c552 (21)

Paracoccus denitrificans [TaxId: 266] (5)

1a	d1ql4a_	A:
1b	d1ql4b_	B:
1c	d1ql4c_	C:
1d	d1ql4d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Paracoccus denitrificans. Organism_taxid: 266. (3)

1a	1ql4A00	A:2-100
1b	1ql4B00	B:2-100
1c	1ql4C00	C:2-100
1d	1ql4D00	D:2-100

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cytochrome-c (108)

Family: Cytochrom_C (54)

Paracoccus denitrificans (3)

1a	Cytochrom_C-1ql4D01	D:4-100
1b	Cytochrom_C-1ql4D02	D:4-100
1c	Cytochrom_C-1ql4D03	D:4-100
1d	Cytochrom_C-1ql4D04	D:4-100

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CY552_PARDE | P54820)

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:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	CY552_PARDE \| P54820	:	1c7m 1i6d 1i6e 1ql3 1zyy 3m97

1ql3	STRUCTURE OF THE SOLUBLE DOMAIN OF CYTOCHROME C552 FROM PARACOCCUS DENITRIFICANS IN THE REDUCED STATE

Description

Compounds

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Ligands, Modified Residues, Ions (1, 4)

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