2C1D - JenaLib

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)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SOXXA FROM P. PANTOTROPHUS

Authors :   T. Dambe, A. Quentmeier, D. Rother, C. Friedrich, A. J. Scheidig

Date :   13 Sep 05 (Deposition) - 06 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

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

Keywords :   Sulfur Oxidation, Cytochrome-C-Type, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Dambe, A. Quentmeier, D. Rother, C. Friedrich, A. J. Scheidig
Structure Of The Cytochrome Complex Soxxa Of Paracoccus Pantotrophus, A Heme Enzyme Initiating Chemotrophic Sulfur Oxidation.
J. Struct. Biol. V. 152 229 2005
PubMed-ID: 16297640 | Reference-DOI: 10.1016/J.JSB.2005.09.002

Molecule 1 - SOXX
	Chains	:	B, D, F, H
	Engineered	:	YES
	Expression System	:	PARACOCCUS PANTOTROPHUS
	Expression System Taxid	:	82367
	Organism Scientific	:	PARACOCCUS PANTOTROPHUS
	Organism Taxid	:	82367
	Other Details	:	CYTOCHROME C

Molecule 2 - SOXA
	Chains	:	A, C, E, G
	Engineered	:	YES
	Expression System	:	PARACOCCUS PANTOTROPHUS
	Expression System Taxid	:	82367
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Other Details	:	DIHEME CYTOCHROME C

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 28)

No.	Name	Count	Type	Full Name
1	CSS	4	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	HEC	12	Ligand/Ion	HEME C
3	ZN	12	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	HEC	3	Ligand/Ion	HEME C
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	HEC	3	Ligand/Ion	HEME C
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	HEC	3	Ligand/Ion	HEME C
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	HEC	3	Ligand/Ion	HEME C
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:70 , ASP A:74 , HIS A:190 , ASP A:266	BINDING SITE FOR RESIDUE ZN A1293
02	AC2	SOFTWARE	HIS A:129 , HEC A:1291 , HOH A:2335 , HEC E:1291	BINDING SITE FOR RESIDUE ZN A1294
03	AC3	SOFTWARE	ASP A:78 , ASP A:81 , ASP A:265 , HOH A:2081 , HOH A:2306	BINDING SITE FOR RESIDUE ZN A1295
04	AC4	SOFTWARE	HEC A:1291 , HOH A:2336 , HIS E:129 , HEC E:1291	BINDING SITE FOR RESIDUE ZN A1296
05	AC5	SOFTWARE	ASP C:70 , ASP C:74 , HIS C:190 , ASP C:266	BINDING SITE FOR RESIDUE ZN C1293
06	AC6	SOFTWARE	ASP C:78 , ASP C:81 , ASP C:265	BINDING SITE FOR RESIDUE ZN C1294
07	AC7	SOFTWARE	HIS C:129 , HEC C:1291 , HEC G:1291	BINDING SITE FOR RESIDUE ZN C1295
08	AC8	SOFTWARE	ASP E:70 , ASP E:74 , HIS E:190 , ASP E:266	BINDING SITE FOR RESIDUE ZN E1293
09	AC9	SOFTWARE	ASP E:78 , ASP E:81 , ASP E:265 , HOH E:2327	BINDING SITE FOR RESIDUE ZN E1294
10	BC1	SOFTWARE	ASP G:70 , ASP G:74 , HIS G:190 , ASP G:266	BINDING SITE FOR RESIDUE ZN G1293
11	BC2	SOFTWARE	HEC C:1291 , GLU G:128 , HIS G:129 , HEC G:1291 , HOH G:2332	BINDING SITE FOR RESIDUE ZN G1294
12	BC3	SOFTWARE	ASP G:78 , ASP G:81 , ASP G:265	BINDING SITE FOR RESIDUE ZN G1295
13	BC4	SOFTWARE	SER A:105 , CYS A:106 , CYS A:109 , HIS A:110 , ARG A:125 , HIS A:129 , TYR A:139 , CYS A:143 , ARG A:147 , MET A:148 , MET A:163 , ZN A:1294 , ZN A:1296 , HOH A:2156 , HOH A:2330 , HOH A:2336 , CYS E:109 , HIS E:110 , GLU E:128 , HIS E:129 , HEC E:1291 , HOH E:2146	BINDING SITE FOR RESIDUE HEC A1291
14	BC5	SOFTWARE	GLY A:64 , ARG A:68 , SER A:205 , CYS A:206 , CYS A:209 , HIS A:210 , ILE A:218 , ASP A:221 , HIS A:222 , LEU A:223 , SER A:224 , GLY A:226 , GLN A:227 , ILE A:228 , ARG A:247 , PHE A:248 , CSS A:251 , ARG A:289 , HOH A:2266 , HOH A:2332 , HOH A:2333 , HOH A:2334	BINDING SITE FOR RESIDUE HEC A1292
15	BC6	SOFTWARE	MET A:204 , GLY B:59 , CYS B:61 , CYS B:64 , HIS B:65 , ALA B:80 , LEU B:83 , ARG B:89 , TRP B:90 , ILE B:98 , PHE B:106 , THR B:109 , MET B:111 , PRO B:112 , PHE B:114 , VAL B:148 , HOH B:2123 , HOH B:2176	BINDING SITE FOR RESIDUE HEC B1158
16	BC7	SOFTWARE	SER C:105 , CYS C:106 , CYS C:109 , HIS C:110 , MET C:116 , ARG C:125 , HIS C:129 , TYR C:139 , CYS C:143 , ARG C:147 , MET C:148 , MET C:163 , ZN C:1295 , HOH C:2175 , HOH C:2352 , HOH C:2353 , CYS G:109 , HIS G:110 , GLU G:128 , HIS G:129 , HEC G:1291 , ZN G:1294 , HOH G:2143	BINDING SITE FOR RESIDUE HEC C1291
17	BC8	SOFTWARE	GLY C:64 , ARG C:68 , SER C:205 , CYS C:206 , CYS C:209 , HIS C:210 , ILE C:218 , ASP C:221 , HIS C:222 , LEU C:223 , SER C:224 , GLY C:226 , GLN C:227 , ILE C:228 , ARG C:247 , PHE C:248 , CSS C:251 , VAL C:252 , ARG C:289 , HOH C:2294 , HOH C:2317 , HOH C:2354 , HOH C:2355 , HOH C:2356	BINDING SITE FOR RESIDUE HEC C1292
18	BC9	SOFTWARE	MET C:204 , GLY D:59 , CYS D:61 , CYS D:64 , HIS D:65 , ALA D:80 , LEU D:83 , ARG D:89 , TRP D:90 , ILE D:98 , THR D:109 , MET D:111 , PRO D:112 , PHE D:114 , VAL D:148 , HOH D:2140 , HOH D:2205 , HOH D:2206	BINDING SITE FOR RESIDUE HEC D1158
19	CC1	SOFTWARE	CYS A:109 , HIS A:110 , GLU A:128 , HIS A:129 , HEC A:1291 , ZN A:1294 , ZN A:1296 , HOH A:2139 , SER E:105 , CYS E:106 , CYS E:109 , HIS E:110 , MET E:116 , ARG E:125 , HIS E:129 , TYR E:139 , CYS E:143 , ARG E:147 , MET E:148 , MET E:163 , HOH E:2343 , HOH E:2344	BINDING SITE FOR RESIDUE HEC E1291
20	CC2	SOFTWARE	GLY E:64 , ARG E:68 , SER E:205 , CYS E:206 , CYS E:209 , HIS E:210 , ASP E:221 , HIS E:222 , LEU E:223 , SER E:224 , GLY E:226 , GLN E:227 , ILE E:228 , ARG E:247 , PHE E:248 , CSS E:251 , ARG E:289 , HOH E:2308 , HOH E:2345 , HOH E:2347 , HOH E:2348 , HOH E:2349	BINDING SITE FOR RESIDUE HEC E1292
21	CC3	SOFTWARE	MET E:204 , GLY F:59 , CYS F:61 , CYS F:64 , HIS F:65 , ALA F:80 , LEU F:83 , ARG F:89 , TRP F:90 , ILE F:98 , PHE F:110 , MET F:111 , PRO F:112 , PHE F:114 , VAL F:148 , HOH F:2187 , HOH F:2188 , HOH F:2190 , HOH F:2191	BINDING SITE FOR RESIDUE HEC F1158
22	CC4	SOFTWARE	CYS C:109 , HIS C:110 , GLU C:128 , HIS C:129 , HEC C:1291 , ZN C:1295 , SER G:105 , CYS G:106 , CYS G:109 , HIS G:110 , MET G:116 , ARG G:125 , HIS G:129 , TYR G:139 , CYS G:143 , ARG G:147 , MET G:148 , MET G:163 , ZN G:1294 , HOH G:2159 , HOH G:2177 , HOH G:2328	BINDING SITE FOR RESIDUE HEC G1291
23	CC5	SOFTWARE	GLY G:64 , ARG G:68 , MET G:204 , SER G:205 , CYS G:206 , CYS G:209 , HIS G:210 , ASP G:221 , HIS G:222 , LEU G:223 , SER G:224 , GLY G:226 , GLN G:227 , ILE G:228 , ARG G:247 , PHE G:248 , CSS G:251 , VAL G:252 , ARG G:289 , HOH G:2275 , HOH G:2329 , HOH G:2330 , HOH G:2331	BINDING SITE FOR RESIDUE HEC G1292
24	CC6	SOFTWARE	MET G:204 , GLY H:59 , CYS H:61 , CYS H:64 , HIS H:65 , ALA H:80 , LEU H:83 , ARG H:89 , TRP H:90 , ILE H:98 , PHE H:106 , THR H:109 , PHE H:110 , MET H:111 , PRO H:112 , PHE H:114 , VAL H:148 , HOH H:2200 , HOH H:2201	BINDING SITE FOR RESIDUE HEC H1158

(no "SS Bond" information available for 2C1D)

Asymmetric Unit

No.	Residues
1	Met A:123	-	Pro A:124
2	Phe A:231	-	Pro A:232
3	Glu B:134	-	Pro B:135
4	Met C:123	-	Pro C:124
5	Phe C:231	-	Pro C:232
6	Glu D:134	-	Pro D:135
7	Met E:123	-	Pro E:124
8	Phe E:231	-	Pro E:232
9	Glu F:134	-	Pro F:135
10	Met G:123	-	Pro G:124
11	Phe G:231	-	Pro G:232
12	Glu H:134	-	Pro H:135

(no "SAP(SNP)/Variant" information available for 2C1D)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_PARPN	78-171	4	A:78-171 C:78-171 E:78-171 G:78-171
2	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	SOXA_PARPN	101-215	4	A:101-215 C:101-215 E:101-215 G:101-215

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_PARPN	78-171	1	A:78-171 - - -
2	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	SOXA_PARPN	101-215	1	A:101-215 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_PARPN	78-171	1	- C:78-171 - -
2	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	SOXA_PARPN	101-215	1	- C:101-215 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_PARPN	78-171	1	- - E:78-171 -
2	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	SOXA_PARPN	101-215	1	- - E:101-215 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	SOXA_PARPN	78-171	1	- - - G:78-171
2	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	SOXA_PARPN	101-215	1	- - - G:101-215

(no "Exon" information available for 2C1D)

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:264
 aligned with SOXA_PARPN | O33434 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:264
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           SOXA_PARPN    27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGCVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
               SCOP domains d2c1da1 A:27-179 automated matches                                                                                                                       d2c1da2 A:180-290 automated matches                                                                             SCOP domains
               CATH domains 2c1dA01 A:27-84,A:174-290 Cytochrome c                    2c1dA02 A:85-173 Cytochrome c                                                            2c1dA01 A:27-84,A:174-290 Cytochrome c                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eee..ee..hhhhh.....ee.hhhhhhhhhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhh.ee......eehhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.......hhhhhhh.....ee..ee..........eee....eeehhhhhhhhhhhh.........hhhhhhhhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------CYTC  PDB: A:78-171 UniProt: 78-171                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------MULTIHEME_CYTC  PDB: A:101-215 UniProt: 101-215                                                                    --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1d A  27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGcVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    |  256       266       276       286    
                                                                                                                                                                                                                                                          251-CSS

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q9LCV0_PARDE | Q9LCV0 from UniProtKB/TrEMBL  Length:157

    Alignment length:137
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q9LCV0_PARDE    21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
               SCOP domains d2c1db_ B: automated matches                                                                                                              SCOP domains
               CATH domains 2c1dB00 B:21-157 Cytochrome c                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh................hhhhhhhhhh.....hhhhh....................hhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1d B  21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
                                    30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:264
 aligned with SOXA_PARPN | O33434 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:264
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           SOXA_PARPN    27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGCVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
               SCOP domains d2c1dc1 C:27-179 automated matches                                                                                                                       d2c1dc2 C:180-290 automated matches                                                                             SCOP domains
               CATH domains 2c1dC01 C:27-84,C:174-290 Cytochrome c                    2c1dC02 C:85-173 Cytochrome c                                                            2c1dC01 C:27-84,C:174-290 Cytochrome c                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eee..ee..hhhhh.....ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhh.ee......eehhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.......hhhhhhh.....ee..ee..........eee....eeehhhhhhhhhhhh.........hhhhhhhhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------CYTC  PDB: C:78-171 UniProt: 78-171                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------MULTIHEME_CYTC  PDB: C:101-215 UniProt: 101-215                                                                    --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1d C  27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGcVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    |  256       266       276       286    
                                                                                                                                                                                                                                                          251-CSS

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with Q9LCV0_PARDE | Q9LCV0 from UniProtKB/TrEMBL  Length:157

    Alignment length:137
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q9LCV0_PARDE    21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
               SCOP domains d2c1dd_ D: automated matches                                                                                                              SCOP domains
               CATH domains 2c1dD00 D:21-157 Cytochrome c                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh................hhhhhhhhhh.....hhhhh....................hhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1d D  21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
                                    30        40        50        60        70        80        90       100       110       120       130       140       150

Chain E from PDB  Type:PROTEIN  Length:264
 aligned with SOXA_PARPN | O33434 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:264
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           SOXA_PARPN    27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGCVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
               SCOP domains d2c1de1 E:27-179 automated matches                                                                                                                       d2c1de2 E:180-290 automated matches                                                                             SCOP domains
               CATH domains 2c1dE01 E:27-84,E:174-290 Cytochrome c                    2c1dE02 E:85-173 Cytochrome c                                                            2c1dE01 E:27-84,E:174-290 Cytochrome c                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eee..ee..hhhhh.....ee.hhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhh.ee......eehhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhh.....ee..ee..........eee....eeehhhhhhhhhhhh.........hhhhhhhhhhhhhh.........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------CYTC  PDB: E:78-171 UniProt: 78-171                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------MULTIHEME_CYTC  PDB: E:101-215 UniProt: 101-215                                                                    --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1d E  27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGcVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    |  256       266       276       286    
                                                                                                                                                                                                                                                          251-CSS

Chain F from PDB  Type:PROTEIN  Length:137
 aligned with Q9LCV0_PARDE | Q9LCV0 from UniProtKB/TrEMBL  Length:157

    Alignment length:137
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q9LCV0_PARDE    21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
               SCOP domains d2c1df_ F: automated matches                                                                                                              SCOP domains
               CATH domains 2c1dF00 F:21-157 Cytochrome c                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh................hhhhhhhhhh.....hhhhh....................hhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1d F  21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
                                    30        40        50        60        70        80        90       100       110       120       130       140       150

Chain G from PDB  Type:PROTEIN  Length:264
 aligned with SOXA_PARPN | O33434 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:264
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286    
           SOXA_PARPN    27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGCVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
               SCOP domains d2c1dg1 G:27-179 automated matches                                                                                                                       d2c1dg2 G:180-290 automated matches                                                                             SCOP domains
               CATH domains 2c1dG01 G:27-84,G:174-290 Cytochrome c                    2c1dG02 G:85-173 Cytochrome c                                                            2c1dG01 G:27-84,G:174-290 Cytochrome c                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eee..ee..hhhhh.....ee.hhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhh.ee......eehhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.......hhhhhhh.....ee..ee..........eee....eeehhhhhhhhhhhh.........hhhhhhhhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------CYTC  PDB: G:78-171 UniProt: 78-171                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------MULTIHEME_CYTC  PDB: G:101-215 UniProt: 101-215                                                                    --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1d G  27 DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGcVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH 290
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    |  256       266       276       286    
                                                                                                                                                                                                                                                          251-CSS

Chain H from PDB  Type:PROTEIN  Length:137
 aligned with Q9LCV0_PARDE | Q9LCV0 from UniProtKB/TrEMBL  Length:157

    Alignment length:137
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q9LCV0_PARDE    21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
               SCOP domains d2c1dh_ H: automated matches                                                                                                              SCOP domains
               CATH domains 2c1dH00 H:21-157 Cytochrome c                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh................hhhhhhhhhh.....hhhhh....................hhhhhhhhhhhhhhhhhhhhh...................................hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1d H  21 CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE 157
                                    30        40        50        60        70        80        90       100       110       120       130       140       150

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: automated matches (31)

Protein domain: automated matches (31)

Paracoccus denitrificans [TaxId: 266] (1)

1a	d2c1da1	A:27-179
1b	d2c1da2	A:180-290
1c	d2c1dc1	C:27-179
1d	d2c1dc2	C:180-290
1e	d2c1de1	E:27-179
1f	d2c1de2	E:180-290
1g	d2c1dg1	G:27-179
1h	d2c1dg2	G:180-290

Paracoccus pantotrophus [TaxId: 82367] (3)

2a	d2c1db_	B:
2b	d2c1dd_	D:
2c	d2c1df_	F:
2d	d2c1dh_	H:

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 pantotrophus. Organism_taxid: 82367. (2)

1a	2c1dB00	B:21-157
1b	2c1dD00	D:21-157
1c	2c1dA01	A:27-84,A:174-290
1d	2c1dC01	C:27-84,C:174-290
1e	2c1dE01	E:27-84,E:174-290
1f	2c1dG01	G:27-84,G:174-290
1g	2c1dF00	F:21-157
1h	2c1dH00	H:21-157
1i	2c1dA02	A:85-173
1j	2c1dC02	C:85-173
1k	2c1dE02	E:85-173
1l	2c1dG02	G:85-173

(no "Pfam Domain" information available for 2C1D)

Asymmetric Unit(hide GO term definitions)

Chain A,C,E,G (SOXA_PARPN | O33434)

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: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: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).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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,F,H (Q9LCV0_PARDE | Q9LCV0)


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
	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
		CSS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:134 - Pro B:135	[ RasMol ]
		Glu D:134 - Pro D:135	[ RasMol ]
		Glu F:134 - Pro F:135	[ RasMol ]
		Glu H:134 - Pro H:135	[ RasMol ]
		Met A:123 - Pro A:124	[ RasMol ]
		Met C:123 - Pro C:124	[ RasMol ]
		Met E:123 - Pro E:124	[ RasMol ]
		Met G:123 - Pro G:124	[ RasMol ]
		Phe A:231 - Pro A:232	[ RasMol ]
		Phe C:231 - Pro C:232	[ RasMol ]
		Phe E:231 - Pro E:232	[ RasMol ]
		Phe G:231 - Pro G:232	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 \| Biol. Unit 4 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
	2c1d
		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
	Q9LCV0_PARDE \| Q9LCV0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	SOXA_PARPN \| O33434
		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
	Q9LCV0_PARDE \| Q9LCV0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	SOXA_PARPN \| O33434
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2C1D)

(no "Related Entries Specified in the PDB File" available for 2C1D)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 28)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 12)

CATH Domains (1, 12)

Pfam Domains (0, 0)

Gene Ontology (14, 17)

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