1QL3 - JenaLib

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

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

Date :   20 Aug 99 (Deposition) - 06 Feb 00 (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 Protein (Cytochrome), Electron Transfer, Reduced (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 , PRO A:28 , LEU A:30 , ARG A:36 , ALA A:39 , TYR A:46 , SER A:47 , 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:2157	BINDING SITE FOR RESIDUE HEC A 101
2	AC2	SOFTWARE	LEU A:20 , LYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , VAL B:26 , PRO B:28 , LEU B:30 , 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 , LEU B:92 , HOH B:2094	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 , LEU C:30 , ARG C:36 , ALA C:39 , TYR C:46 , SER C:47 , MET C:50 , TRP C:57 , LEU C:62 , THR C:76 , LYS C:77 , MET C:78 , ALA C:79 , LEU C:92 , HOH C:2060	BINDING SITE FOR RESIDUE HEC C 101
4	AC4	SOFTWARE	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 , MET D:50 , TRP D:57 , LEU D:62 , PHE D:65 , LEU D:66 , THR D:76 , LYS D:77 , MET D:78 , PHE D:80 , LEU D:92 , HOH D:2102	BINDING SITE FOR RESIDUE HEC D 101

(no "SS Bond" information available for 1QL3)

(no "Cis Peptide Bond" information available for 1QL3)

(no "SAP(SNP)/Variant" information available for 1QL3)

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 1QL3)

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 d1ql3a_ A: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql3A00 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
                 1ql3 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 d1ql3b_ B: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql3B00 B:2-100 Cytochrome c                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:2-100 UniProt: 78-176                                                                  PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1ql3 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 d1ql3c_ C: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql3C00 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
                 1ql3 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 d1ql3d_ D: Cytochrome c552                                                                          SCOP domains
               CATH domains 1ql3D00 D:2-100 Cytochrome c                                                                        CATH domains
           Pfam domains (1) --Cytochrom_C-1ql3D01 D:4-100                                                                       Pfam domains (1)
           Pfam domains (2) --Cytochrom_C-1ql3D02 D:4-100                                                                       Pfam domains (2)
           Pfam domains (3) --Cytochrom_C-1ql3D03 D:4-100                                                                       Pfam domains (3)
           Pfam domains (4) --Cytochrom_C-1ql3D04 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
                 1ql3 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	d1ql3a_	A:
1b	d1ql3b_	B:
1c	d1ql3c_	C:
1d	d1ql3d_	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	1ql3A00	A:2-100
1b	1ql3B00	B:2-100
1c	1ql3C00	C:2-100
1d	1ql3D00	D:2-100

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cytochrome-c (108)

Family: Cytochrom_C (54)

Paracoccus denitrificans (3)

1a	Cytochrom_C-1ql3D01	D:4-100
1b	Cytochrom_C-1ql3D02	D:4-100
1c	Cytochrom_C-1ql3D03	D:4-100
1d	Cytochrom_C-1ql3D04	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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	1ql3
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	CY552_PARDE \| P54820	:	1c7m 1i6d 1i6e 1ql4 1zyy 3m97

1ql4	STRUCTURE OF THE SOLUBLE DOMAIN OF CYTOCHROME C552 FROM PARACOCCUS DENITRIFICANS IN THE OXIDISED STATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

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