3OCD - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   DIHEME SOXAX - C236M MUTANT

Authors :   M. J. Maher

Date :   09 Aug 10 (Deposition) - 18 May 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Cytochrome, Thiosulfate Oxidation Pathway, Heme-Binding Protein-Heme- Binding Protein Complex, Heme-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kilmartin, M. J. Maher, K. Krusong, G. R. Hanson, P. V. Bernhardt, M. Riley, U. Kappler
Diheme Soxax Proteins - Insights Into Structure And Functio Of The Active Site
To Be Published
PubMed: search

Molecule 1 - SOXA
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	RHODOBACTER CAPSULATUS
	Expression System Taxid	:	1061
	Mutation	:	YES
	Organism Scientific	:	STARKEYA NOVELLA
	Organism Taxid	:	921

Molecule 2 - SOXX
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	RHODOBACTER CAPSULATUS
	Expression System Taxid	:	1061
	Organism Scientific	:	STARKEYA NOVELLA
	Organism Taxid	:	921

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

No.	Name	Count	Type	Full Name
1	HEC	2	Ligand/Ion	HEME C

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HEC	2	Ligand/Ion	HEME C

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:183 , CYS A:186 , HIS A:187 , ILE A:194 , LEU A:199 , THR A:212 , TRP A:216 , ARG A:220 , ARG A:232 , MET A:233 , MET A:236 , TYR A:237 , MET A:240 , LYS A:274	BINDING SITE FOR RESIDUE HEC A 401
2	AC2	SOFTWARE	PHE A:181 , GLY B:123 , CYS B:125 , CYS B:128 , HIS B:129 , LEU B:141 , PRO B:143 , LEU B:145 , TYR B:148 , ARG B:152 , LYS B:165 , VAL B:166 , LEU B:173 , SER B:176 , SER B:177 , MET B:178 , PRO B:179 , PHE B:181	BINDING SITE FOR RESIDUE HEC B 401
3	AC3	SOFTWARE	PHE C:181 , SER C:182 , CYS C:183 , CYS C:186 , HIS C:187 , ILE C:194 , GLN C:197 , LEU C:199 , PRO C:200 , THR C:212 , TRP C:216 , ARG C:220 , ARG C:232 , MET C:233 , MET C:236 , TYR C:237 , GLN C:239 , MET C:240 , LYS C:274	BINDING SITE FOR RESIDUE HEC C 401
4	AC4	SOFTWARE	LYS B:81 , PHE C:181 , GLY D:123 , ASN D:124 , CYS D:125 , CYS D:128 , HIS D:129 , LEU D:145 , TYR D:148 , LYS D:165 , VAL D:166 , LEU D:173 , SER D:177 , MET D:178 , PRO D:179 , PHE D:181 , LEU D:187 , VAL D:195	BINDING SITE FOR RESIDUE HEC D 401

Asymmetric Unit

No.	Residues
1	A:74	-	A:110
2	B:64	-	B:175
3	C:74	-	C:110
4	D:64	-	D:175

Asymmetric Unit

No.	Residues
1	Leu A:90	-	Pro A:91
2	Trp A:216	-	Pro A:217
3	Val A:270	-	Pro A:271
4	Leu C:90	-	Pro C:91
5	Trp C:216	-	Pro C:217
6	Val C:270	-	Pro C:271

(no "SAP(SNP)/Variant" information available for 3OCD)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_STAND	163-263	2	A:163-263 C:163-263

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_STAND	163-263	1	A:163-263 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_STAND	163-263	1	- C:163-263

(no "Exon" information available for 3OCD)

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:229
 aligned with SOXA_STAND | D7A6E5 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:229
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265         
           SOXA_STAND    46 ANPGFLNVDRGEVLWSEPRGTRNVSLETCDLGEGPGKLEGAYAHLPRYFADTGKVMDLEQRLLWCMETIQGRDTKPLVAKPFSGPGRTSDMEDLVAFIANKSDGVKIKVALATPQEKEMYAIGEALFFRRSSINDFSCSTCHGAAGKRIRLQALPQLDVPGKDAQLTMATWPTYRVSQSALRTMQHRMWDCYRQMRMPAPDYASEAVTALTLYLTKQAEGGELKVPSIK 274
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......................hhhhhh.ee......eehhhhhhhhhhhhh......................hhhhhhhhhh...........hhhhhhhhhhhhhhhhh.......hhhhhh.....ee..ee.......hhhhhhhhh...eee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------CYTC  PDB: A:163-263 UniProt: 163-263                                                                ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ocd A  46 ANPGFLNVDRGEVLWSEPRGTRNVSLETCDLGEGPGKLEGAYAHLPRYFADTGKVMDLEQRLLWCMETIQGRDTKPLVAKPFSGPGRTSDMEDLVAFIANKSDGVKIKVALATPQEKEMYAIGEALFFRRSSINDFSCSTCHGAAGKRIRLQALPQLDVPGKDAQLTMATWPTYRVSQSALRTMQHRMWDMYRQMRMPAPDYASEAVTALTLYLTKQAEGGELKVPSIK 274
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with Q7BQR5_STANO | Q7BQR5 from UniProtKB/TrEMBL  Length:208

    Alignment length:180
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
         Q7BQR5_STANO    29 SAVDPARVDAVVKTSFTKLPEGWESRLQQDETQRICSVTRNNPSPEQAAAIMKAEEVRIKFPAGPVLGSWKDGAKVAQNGRGGQFSDPPGTVSGGNCYACHQLDPKEVSYGTLGPSLVGYGRERNFSAEDAKIAFAKVYDAQASLACSSMPRFGVNGVLTEQQIKDVVAYLFDPESPVNK 208
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhh......hhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhh.........hhhhhhhhhhh................hhhhh..................hhhhhh..hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ocd B  29 SAVDPARVDAVVKTSFTKLPEGWESRLQQDETQRICSVTRNNPSPEQAAAIMKAEEVRIKFPAGPVLGSWKDGAKVAQNGRGGQFSDPPGTVSGGNCYACHQLDPKEVSYGTLGPSLVGYGRERNFSAEDAKIAFAKVYDAQASLACSSMPRFGVNGVLTEQQIKDVVAYLFDPESPVNK 208
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with SOXA_STAND | D7A6E5 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:229
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265         
           SOXA_STAND    46 ANPGFLNVDRGEVLWSEPRGTRNVSLETCDLGEGPGKLEGAYAHLPRYFADTGKVMDLEQRLLWCMETIQGRDTKPLVAKPFSGPGRTSDMEDLVAFIANKSDGVKIKVALATPQEKEMYAIGEALFFRRSSINDFSCSTCHGAAGKRIRLQALPQLDVPGKDAQLTMATWPTYRVSQSALRTMQHRMWDCYRQMRMPAPDYASEAVTALTLYLTKQAEGGELKVPSIK 274
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhh.................................hhhhhhhhhhhhhh...hhhhhh.........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.hhhhh..hhhhhh....ee..ee.......hhhhhhhhh...eee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhh........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------CYTC  PDB: C:163-263 UniProt: 163-263                                                                ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ocd C  46 ANPGFLNVDRGEVLWSEPRGTRNVSLETCDLGEGPGKLEGAYAHLPRYFADTGKVMDLEQRLLWCMETIQGRDTKPLVAKPFSGPGRTSDMEDLVAFIANKSDGVKIKVALATPQEKEMYAIGEALFFRRSSINDFSCSTCHGAAGKRIRLQALPQLDVPGKDAQLTMATWPTYRVSQSALRTMQHRMWDMYRQMRMPAPDYASEAVTALTLYLTKQAEGGELKVPSIK 274
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

Chain D from PDB  Type:PROTEIN  Length:180
 aligned with Q7BQR5_STANO | Q7BQR5 from UniProtKB/TrEMBL  Length:208

    Alignment length:180
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
         Q7BQR5_STANO    29 SAVDPARVDAVVKTSFTKLPEGWESRLQQDETQRICSVTRNNPSPEQAAAIMKAEEVRIKFPAGPVLGSWKDGAKVAQNGRGGQFSDPPGTVSGGNCYACHQLDPKEVSYGTLGPSLVGYGRERNFSAEDAKIAFAKVYDAQASLACSSMPRFGVNGVLTEQQIKDVVAYLFDPESPVNK 208
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------Cytochrom_C-3ocdD01 D:99-201                                                                           ------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------Cytochrom_C-3ocdD02 D:99-201                                                                           ------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhh......hhhhh..hhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhh................hhhhh..........................hhhhhhhhhhhhhh...........hhhhhh..hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ocd D  29 SAVDPARVDAVVKTSFTKLPEGWESRLQQDETQRICSVTRNNPSPEQAAAIMKAEEVRIKFPAGPVLGSWKDGAKVAQNGRGGQFSDPPGTVSGGNCYACHQLDPKEVSYGTLGPSLVGYGRERNFSAEDAKIAFAKVYDAQASLACSSMPRFGVNGVLTEQQIKDVVAYLFDPESPVNK 208
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

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 '\|'

(no "SCOP Domain" information available for 3OCD)

(no "CATH Domain" information available for 3OCD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cytochrome-c (108)

Family: Cytochrom_C (54)

Starkeya novella (Thiobacillus novellus) (2)

1a	Cytochrom_C-3ocdD01	D:99-201
1b	Cytochrom_C-3ocdD02	D:99-201

Asymmetric Unit(hide GO term definitions)

Chain A,C (SOXA_STAND | D7A6E5)

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:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016669	oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces a cytochrome.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0016783	sulfurtransferase activity	Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
biological process
	GO:0018192	enzyme active site formation via cysteine modification to L-cysteine persulfide	The formation of an enzyme active site via modification of peptidyl-cysteine to peptidyl-L-cysteine persulfide.
	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.
	GO:0019417	sulfur oxidation	The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur.
cellular component
	GO:0070069	cytochrome complex	A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
	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).

Chain B,D (Q7BQR5_STANO | Q7BQR5)


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.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu A:90 - Pro A:91	[ RasMol ]
		Leu C:90 - Pro C:91	[ RasMol ]
		Trp A:216 - Pro A:217	[ RasMol ]
		Trp C:216 - Pro C:217	[ RasMol ]
		Val A:270 - Pro A:271	[ RasMol ]
		Val C:270 - Pro C:271	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	SOXA_STAND \| D7A6E5	:	3oa8
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	Q7BQR5_STANO \| Q7BQR5	:	3oa8

3oa8	DIHEME SOXAX, WILD FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (15, 18)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File