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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE CYTOCHROME C PEROXIDASE
 
Authors :  M. Fischer, J. S. Fraser
Date :  26 Jan 15  (Deposition) - 25 Feb 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,C,E,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  G  (1x)
Keywords :  Model System, Flexibility, Thermodynamics, Cryptic Site, Transient Protein Sites, Ligand Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fischer, B. K. Shoichet, J. S. Fraser
One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding To Transient Protein Sites.
Chembiochem V. 16 1560 2015
PubMed-ID: 26032594  |  Reference-DOI: 10.1002/CBIC.201500196
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE, MITOCHONDRIAL
    Chains: A, C, E, G
    EC Number: 1.11.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 69-361
    Gene: CCP1, CCP, CPO, YKR066C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: CCP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACEG
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  C  
Biological Unit 3 (1x):   E 
Biological Unit 4 (1x):    G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1BZI3Ligand/IonBENZIMIDAZOLE
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BZI1Ligand/IonBENZIMIDAZOLE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BZI1Ligand/IonBENZIMIDAZOLE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1BZI1Ligand/IonBENZIMIDAZOLE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1BZI-1Ligand/IonBENZIMIDAZOLE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:44 , ARG A:48 , TRP A:51 , PRO A:145 , ASP A:146 , LEU A:171 , MET A:172 , ALA A:174 , HIS A:175 , GLY A:178 , LYS A:179 , THR A:180 , HIS A:181 , ASN A:184 , SER A:185 , TRP A:191 , LEU A:232 , HOH A:1313 , HOH A:1320 , HOH A:1322 , HOH A:1343binding site for residue HEM A 1201
2AC2SOFTWAREPHE A:89 , LEU A:92 , GLU A:93 , HIS A:96 , SER A:104 , LEU A:107 , PHE A:108binding site for residue BZI A 1202
3AC3SOFTWAREPRO C:44 , ARG C:48 , TRP C:51 , PRO C:145 , ASP C:146 , ALA C:174 , HIS C:175 , GLY C:178 , LYS C:179 , THR C:180 , HIS C:181 , ASN C:184 , SER C:185 , TRP C:191 , LEU C:232 , HOH C:1331 , HOH C:1335 , HOH C:1375binding site for residue HEM C 1201
4AC4SOFTWAREPHE C:89 , LEU C:92 , GLU C:93 , HIS C:96 , SER C:104 , PHE C:108binding site for residue BZI C 1202
5AC5SOFTWAREPRO E:44 , VAL E:47 , ARG E:48 , TRP E:51 , PRO E:145 , ASP E:146 , LEU E:171 , ALA E:174 , HIS E:175 , GLY E:178 , LYS E:179 , THR E:180 , HIS E:181 , ASN E:184 , SER E:185 , TRP E:191 , LEU E:232 , HOH E:1346 , HOH E:1372binding site for residue HEM E 1201
6AC6SOFTWAREPHE E:89 , GLU E:93 , HIS E:96 , SER E:104binding site for residue BZI E 1202
7AC7SOFTWAREPRO G:44 , ARG G:48 , TRP G:51 , PRO G:145 , LEU G:171 , MET G:172 , ALA G:174 , HIS G:175 , LYS G:179 , THR G:180 , HIS G:181 , ASN G:184 , SER G:185 , TRP G:191 , LEU G:232 , HOH G:1309binding site for residue HEM G 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XVA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XVA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XVA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XVA)

(-) Exons   (0, 0)

(no "Exon" information available for 4XVA)

(-) Sequences/Alignments

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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.............hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xva A   2 TPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   


Chain C from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhh.............hhhhhhhhhh..eeee.....eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.............hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xva C   3 PLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  


Chain E from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh.ee........ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xva E   2 TPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   


Chain G from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eeeee.....eeeee....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xva G   3 PLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 294
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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  (0, 0)

(no "SCOP Domain" information available for 4XVA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XVA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XVA)

(-) Gene Ontology  (14, 14)

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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        CCPR_YEAST | P00431: 1a2f 1a2g 1aa4 1ac4 1ac8 1aeb 1aed 1aee 1aef 1aeg 1aeh 1aej 1aek 1aem 1aen 1aeo 1aeq 1aes 1aet 1aeu 1aev 1bej 1bek 1bem 1bep 1beq 1bes 1bj9 1bva 1cca 1ccb 1ccc 1cce 1ccg 1cci 1ccj 1cck 1ccl 1ccp 1cmp 1cmq 1cmt 1cmu 1cpd 1cpe 1cpf 1cpg 1cyf 1dcc 1dj1 1dj5 1ds4 1dse 1dsg 1dso 1dsp 1ebe 1jci 1jdr 1kok 1krj 1kxm 1kxn 1mk8 1mkq 1mkr 1ml2 1ryc 1s6v 1s73 1sbm 1sdq 1sog 1stq 1u74 1u75 1z53 1zby 1zbz 2anz 2aqd 2as1 2as2 2as3 2as4 2as6 2b0z 2b10 2b11 2b12 2bcn 2ccp 2cep 2cyp 2eun 2euo 2eup 2euq 2eur 2eus 2eut 2euu 2gb8 2ia8 2icv 2jti 2n18 2pcb 2pcc 2rbt 2rbu 2rbv 2rbw 2rbx 2rby 2rbz 2rc0 2rc1 2rc2 2v23 2v2e 2x07 2x08 2xil 2xj5 2xj8 2y5a 2ycg 3ccp 3ccx 3e2n 3e2o 3exb 3m23 3m25 3m26 3m27 3m28 3m29 3m2a 3m2b 3m2c 3m2d 3m2e 3m2f 3m2g 3m2h 3m2i 3r98 3r99 4a6z 4a71 4a78 4a7m 4ccp 4ccx 4cvi 4cvj 4jb4 4nfg 4p4q 4xv4 4xv5 4xv6 4xv7 4xv8 5ccp 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5d6m 5ejt 5ejx 6ccp 7ccp

(-) Related Entries Specified in the PDB File

4xv4 4xv5 4xv6 4xv7 4xv8 4xva