1DW2 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE NITRIC OXIDE COMPLEX OF REDUCED SHP, AN OXYGEN BINDING CYTOCHROME C

Authors :   D. Leys, K. Backers, T. E. Meyer, W. R. Hagen, M. A. Cusanovich, J. J. Van Beeumen

Date :   24 Jan 00 (Deposition) - 28 Jun 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Cytochrome C, Nitric Oxide, Disulfide Bridge, Asparagine Ligation, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Leys, K. Backers, T. E. Meyer, W. R. Hagen, M. A. Cusanovich, J. J. Van Beeumen
Crystal Structures Of An Oxygen-Binding Cytochrome C From Rhodobacter Sphaeroides.
J. Biol. Chem. V. 275 16050 2000
PubMed-ID: 10821858 | Reference-DOI: 10.1074/JBC.275.21.16050
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C
	Chains	:	A, B, C
	Organism Scientific	:	RHODOBACTER SPHAEROIDES
	Organism Taxid	:	1063

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NO	3	Ligand/Ion	NITRIC OXIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NO	-1	Ligand/Ion	NITRIC OXIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NO	-1	Ligand/Ion	NITRIC OXIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NO	-1	Ligand/Ion	NITRIC OXIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:43 , CYS A:46 , HIS A:47 , ARG A:74 , PHE A:75 , ARG A:80 , VAL A:81 , TRP A:84 , ASN A:88 , VAL A:92 , NO A:114 , HOH A:123 , HOH A:137 , HOH A:157 , HOH A:187	BINDING SITE FOR RESIDUE HEM A 113
2	AC2	SOFTWARE	TRP A:84 , ASN A:88 , HEM A:113	BINDING SITE FOR RESIDUE NO A 114
3	AC3	SOFTWARE	CYS B:43 , CYS B:46 , HIS B:47 , ARG B:74 , PHE B:75 , ARG B:80 , VAL B:81 , TRP B:84 , ASN B:88 , LEU B:105 , NO B:114 , HOH B:122 , HOH B:135 , HOH B:172	BINDING SITE FOR RESIDUE HEM B 113
4	AC4	SOFTWARE	TRP B:84 , LEU B:85 , ASN B:88 , HEM B:113	BINDING SITE FOR RESIDUE NO B 114
5	AC5	SOFTWARE	CYS C:43 , CYS C:46 , HIS C:47 , ARG C:58 , ILE C:63 , ARG C:74 , PHE C:75 , ARG C:80 , TRP C:84 , ASN C:88 , LEU C:105 , NO C:114 , HOH C:132 , HOH C:146	BINDING SITE FOR RESIDUE HEM C 113
6	AC6	SOFTWARE	TRP C:84 , LEU C:85 , ASN C:88 , HEM C:113	BINDING SITE FOR RESIDUE NO C 114

Asymmetric Unit

No.	Residues
1	A:89	-	A:97
2	B:89	-	B:97
3	C:89	-	C:97

(no "Cis Peptide Bond" information available for 1DW2)

(no "SAP(SNP)/Variant" information available for 1DW2)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	3	A:20-112 B:20-112 C:20-112

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	1	A:20-112 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	1	- B:20-112 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SHP_RHOS4	37-129	1	- - C:20-112

(no "Exon" information available for 1DW2)

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:112
 aligned with SHP_RHOS4 | P81238 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:112
                                    27        37        47        57        67        77        87        97       107       117       127  
            SHP_RHOS4    18 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 129
               SCOP domains d1dw2a_ A: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw2A00 A:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhh......ee.....ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CYTC  PDB: A:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw2 A   1 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 112
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with SHP_RHOS4 | P81238 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:112
                                    27        37        47        57        67        77        87        97       107       117       127  
            SHP_RHOS4    18 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 129
               SCOP domains d1dw2b_ B: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw2B00 B:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhh......ee.....ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CYTC  PDB: B:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw2 B   1 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 112
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with SHP_RHOS4 | P81238 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:112
                                    27        37        47        57        67        77        87        97       107       117       127  
            SHP_RHOS4    18 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 129
               SCOP domains d1dw2c_ C: SHP, an oxygen binding cytochrome c                                                                   SCOP domains
               CATH domains 1dw2C00 C:1-112 Cytochrome c                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhh......ee.....ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CYTC  PDB: C:20-112 UniProt: 37-129                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dw2 C   1 GDTSPAQLIAGYEAAAGAPADAERGRALFLSTQTGGKPDTPSCTTCHGADVTRAGQTRTGKEIAPLAPSATPDRFTDSARVEKWLGRNCNSVIGRDCTPGEKADLLAWLAAQ 112
                                    10        20        30        40        50        60        70        80        90       100       110

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: SHP, an oxygen binding cytochrome c (4)

Rhodobacter sphaeroides [TaxId: 1063] (4)

1a	d1dw2a_	A:
1b	d1dw2b_	B:
1c	d1dw2c_	C:

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)

Rhodobacter sphaeroides. Organism_taxid: 1063 (7)

1a	1dw2A00	A:1-112
1b	1dw2B00	B:1-112
1c	1dw2C00	C:1-112

(no "Pfam Domain" information available for 1DW2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SHP_RHOS4 | P81238)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dw2)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1dw2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SHP_RHOS4 \| P81238
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SHP_RHOS4 \| P81238
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SHP_RHOS4 \| P81238	:	1dw0 1dw1 1dw3

1dw0	STRUCTURE OF OXIDIZED UNCOMPLEXED SHP
1dw1	STRUCTURE OF CYANIDE COMPLEX OF SHP
1dw3	STRUCTURE OF REDUCED SHP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File