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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - MIXED VALENCE FORM
 
Authors :  A. Echalier, V. Fulop
Date :  21 Sep 05  (Deposition) - 13 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transport, Heme, Oxidoreductase, Periplasmic, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Echalier, C. F. Goodhew, G. W. Pettigrew, V. Fulop
Activation And Catalysis Of The Di-Heme Cytochrome C Peroxidase From Paracoccus Pantotrophus
Structure V. 14 107 2006
PubMed-ID: 16407070  |  Reference-DOI: 10.1016/J.STR.2005.09.011

(-) Compounds

Molecule 1 - DI-HAEM CYTOCHROME C PEROXIDASE
    ChainsA, B
    EC Number1.11.1.5
    Organism ScientificPARACOCCUS PANTOTROPHUS
    Organism Taxid82367

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3HEC4Ligand/IonHEME C

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:93 , THR A:270 , PRO A:272 , HOH A:2191 , HOH A:2415 , HOH A:2500 , HOH A:2501BINDING SITE FOR RESIDUE CA A 403
02AC2SOFTWAREASN B:93 , THR B:270 , PRO B:272 , HOH B:2218 , HOH B:2446 , HOH B:2539 , HOH B:2540BINDING SITE FOR RESIDUE CA B 403
03AC3SOFTWAREILE A:63 , SER A:64 , CYS A:65 , CYS A:68 , HIS A:69 , SER A:82 , GLY A:84 , ARG A:92 , PRO A:95 , GLN A:106 , PHE A:107 , TRP A:108 , ARG A:111 , LEU A:115 , GLN A:118 , PRO A:122 , GLU A:128 , ILE A:170 , GLU A:174 , ARG A:260 , HOH A:2206 , HOH A:2496 , HOH A:2497 , HOH A:2498 , HOH A:2499BINDING SITE FOR RESIDUE HEC A 401
04AC4SOFTWARETRP A:108 , GLY A:210 , CYS A:211 , CYS A:214 , HIS A:215 , HIS A:226 , PHE A:228 , PHE A:259 , ARG A:260 , ALA A:261 , ALA A:262 , LEU A:264 , TYR A:273 , PHE A:274 , HIS A:275 , LEU A:282 , MET A:289 , GLN A:293 , HOH A:2500 , HOH A:2501 , HOH A:2502 , HOH A:2503BINDING SITE FOR RESIDUE HEC A 402
05AC5SOFTWAREARG A:92 , ASP A:243 , GLU A:248 , HOH A:2497 , HOH A:2504 , HOH A:2505 , HOH A:2506 , HOH A:2507BINDING SITE FOR RESIDUE EDO A1339
06AC6SOFTWAREGLU A:19 , TYR A:216 , GLY A:217 , VAL A:218 , HOH A:2509BINDING SITE FOR RESIDUE EDO A1340
07AC7SOFTWAREILE B:63 , SER B:64 , CYS B:65 , CYS B:68 , HIS B:69 , SER B:82 , GLY B:84 , ARG B:92 , PRO B:95 , GLN B:106 , PHE B:107 , TRP B:108 , ARG B:111 , LEU B:115 , GLN B:118 , PRO B:122 , ILE B:170 , GLU B:174 , ARG B:260 , HOH B:2534 , HOH B:2535 , HOH B:2536 , HOH B:2537 , HOH B:2544BINDING SITE FOR RESIDUE HEC B 401
08AC8SOFTWARETRP B:108 , GLY B:210 , CYS B:211 , CYS B:214 , HIS B:215 , HIS B:226 , PHE B:228 , LEU B:230 , PHE B:259 , ARG B:260 , ALA B:261 , ALA B:262 , LEU B:264 , TYR B:273 , PHE B:274 , HIS B:275 , LEU B:282 , MET B:289 , GLN B:293 , HOH B:2440 , HOH B:2538 , HOH B:2539 , HOH B:2540BINDING SITE FOR RESIDUE HEC B 402
09AC9SOFTWAREARG B:92 , ASP B:243 , GLU B:248 , HOH B:2541 , HOH B:2542 , HOH B:2543 , HOH B:2544 , HOH B:2545BINDING SITE FOR RESIDUE EDO B1339
10BC1SOFTWAREALA A:158 , MET B:143 , PRO B:144 , GLU B:145 , PRO B:326 , VAL B:327 , THR B:329 , HOH B:2308 , HOH B:2546BINDING SITE FOR RESIDUE EDO B1340

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C1V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:271 -Pro A:272
2Ala B:271 -Pro B:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C1V)

(-) Exons   (0, 0)

(no "Exon" information available for 2C1V)

(-) Sequences/Alignments

Asymmetric/Biological 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d2c1va1 A:4-180 automated matches                                                                                                                                                d2c1va2 A:181-338 automated matches                                                                                                                            SCOP domains
               CATH domains 2c1vA01 Cytochrome c2c1vA02 A:24-178,A:317-338 Cytochrome c                                                                                                                    2c1vA01 A:4-23,A:179-316 Cytochrome c                                                                                                     2c1vA02 Cytochrome c   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........ee.........ee.hhhhhhhhhhhhhhhhhh.....hhhhhh..............hhhhh..........hhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........eee..................hhhhhhhhhhh.eee.....hhhhh..........hhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1v A   4 AIDNGALREEAKGVFEAIPEKMTAIKQTEDNPEGVPLTAEKIELGKVLFFDPRMSSSGLISCQTCHNVGLGGVDGLPTSIGHGWQKGPRNAPTMLNAIFNAAQFWDGRAADLAEQAKGPVQAGVEMSNTPDQVVKTINSMPEYVEAFKAAFPEEADPVTFDNFAAAIEQFEATLITPNSAFDRFLAGDDAAMTDQEKRGLQAFMETGCTACHYGVNFGGQDYHPFGLIAKPGAEVLPAGDTGRFEVTRTTDDEYVFRAAPLRNVALTAPYFHSGVVWELAEAVKIMSSAQIGTELTDQQAEDITAFLGTLTGEQPVIDHPILPVRTGTTPLPTPM 338
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333     

Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d2c1vb1 B:4-180 automated matches                                                                                                                                                d2c1vb2 B:181-338 automated matches                                                                                                                            SCOP domains
               CATH domains 2c1vB01 Cytochrome c2c1vB02 B:24-178,B:317-338 Cytochrome c                                                                                                                    2c1vB01 B:4-23,B:179-316 Cytochrome c                                                                                                     2c1vB02 Cytochrome c   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh........ee.........ee.hhhhhhhhhhhhhhhhhh.....hhhhhh..............hhhhh..........hhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........eee..................hhhhhhhhhhh.eee.....hhhhh..........hhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1v B   4 AIDNGALREEAKGVFEAIPEKMTAIKQTEDNPEGVPLTAEKIELGKVLFFDPRMSSSGLISCQTCHNVGLGGVDGLPTSIGHGWQKGPRNAPTMLNAIFNAAQFWDGRAADLAEQAKGPVQAGVEMSNTPDQVVKTINSMPEYVEAFKAAFPEEADPVTFDNFAAAIEQFEATLITPNSAFDRFLAGDDAAMTDQEKRGLQAFMETGCTACHYGVNFGGQDYHPFGLIAKPGAEVLPAGDTGRFEVTRTTDDEYVFRAAPLRNVALTAPYFHSGVVWELAEAVKIMSSAQIGTELTDQQAEDITAFLGTLTGEQPVIDHPILPVRTGTTPLPTPM 338
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333     

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C1V)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2C1V)

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  Cis Peptide Bonds
    Ala A:271 - Pro A:272   [ RasMol ]  
    Ala B:271 - Pro B:272   [ RasMol ]  
 

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2c1u CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - OXIDISED FORM