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(-) Description

Title :  CATALASE STRUCTURE DETERMINED BY ELECTRON CRYSTALLOGRAPHY OF THIN 3D CRYSTALS
 
Authors :  K. Yonekura
Date :  04 Jul 16  (Deposition) - 26 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  ELECTRON CRYSTALLOGRAPHY
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Heme, Nadph (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yonekura, M. Maki-Yonekura
Refinement Of Cryo-Em Structures Using Scattering Factors O Charged Atoms
J. Appl. Crystallogr. V. 49 1517 2016
PubMed: search  |  Reference-DOI: 10.1107/S1600576716011274
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATALASE
    Chains: A, B, C, D
    EC Number: 1.11.1.6
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:71 , VAL A:73 , HIS A:74 , ARG A:111 , GLY A:130 , VAL A:145 , ASN A:147 , ALA A:157 , PHE A:160 , SER A:216 , HIS A:217 , LEU A:298 , PHE A:333 , MET A:349 , ARG A:353 , TYR A:357 , THR A:360 , HIS A:361 , ARG A:364 , HOH A:718 , ASP D:64binding site for residue HEM A 601
2AC2SOFTWAREHIS A:193 , PHE A:197 , SER A:200 , ARG A:202 , ASN A:212 , HIS A:234 , LYS A:236 , TRP A:302 , HIS A:304 , GLN A:441 , PHE A:445 , VAL A:449binding site for residue NDP A 602
3AC3SOFTWAREARG B:71 , VAL B:73 , HIS B:74 , ARG B:111 , GLY B:130 , ALA B:132 , VAL B:145 , GLY B:146 , ASN B:147 , PHE B:160 , SER B:216 , PHE B:333 , MET B:349 , ARG B:353 , TYR B:357 , THR B:360 , HIS B:361 , ARG B:364 , HOH B:714 , MET C:60 , ASP C:64binding site for residue HEM B 601
4AC4SOFTWAREHIS B:193 , PHE B:197 , SER B:200 , ARG B:202 , ASN B:212 , LYS B:236 , VAL B:301 , TRP B:302 , HIS B:304 , GLN B:441 , PHE B:445 , VAL B:449binding site for residue NDP B 602
5AC5SOFTWAREMET B:60 , ASP B:64 , ARG C:71 , VAL C:72 , HIS C:74 , ARG C:111 , GLY C:130 , VAL C:145 , GLY C:146 , ASN C:147 , PHE C:160 , HIS C:217 , PHE C:333 , MET C:349 , ARG C:353 , TYR C:357 , THR C:360 , HIS C:361 , ARG C:364 , HOH C:706 , HOH C:716binding site for residue HEM C 601
6AC6SOFTWAREHIS C:193 , PHE C:197 , SER C:200 , ARG C:202 , ASN C:212 , HIS C:234 , LYS C:236 , TRP C:302 , PRO C:303 , HIS C:304 , GLN C:441 , THR C:444 , PHE C:445 , VAL C:449binding site for residue NDP C 602
7AC7SOFTWAREMET A:60 , ASP A:64 , ARG D:71 , VAL D:72 , VAL D:73 , HIS D:74 , ARG D:111 , GLY D:130 , VAL D:145 , GLY D:146 , ASN D:147 , ALA D:157 , PHE D:160 , GLY D:215 , SER D:216 , HIS D:217 , PHE D:333 , ARG D:353 , TYR D:357 , THR D:360 , HIS D:361 , ARG D:364binding site for residue HEM D 601
8AC8SOFTWAREHIS D:193 , PHE D:197 , SER D:200 , ARG D:202 , ASN D:212 , LYS D:236 , VAL D:301 , TRP D:302 , PRO D:303 , HIS D:304 , GLN D:441 , PHE D:445 , VAL D:449 , HOH D:710binding site for residue NDP D 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GKN)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:404 -Pro A:405
2Tyr B:404 -Pro B:405
3Tyr C:404 -Pro C:405
4Tyr D:404 -Pro D:405

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GKN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GKN)

(-) Exons   (0, 0)

(no "Exon" information available for 5GKN)

(-) 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:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh......................eee.........hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh........ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeehhhhhhhh..................eeeeeeeeee...hhhhhh.............eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....................................hhhhh.........eee........hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkn A   3 NRDPASDQMKHWKEQRAAQKPDVLTTGGGNPVGDKLNSLTVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITRYSKAKVFEHIGKRTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDALLFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLAHEDPDYGLRDLFNAIATGNYPSWTLYIQVMTFSEAEIFPFNPFDLTKVWPHGDYPLIPVGKLVLNRNPVNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFAYPDTHRHRLGPNYLQIPVNCPYRARVANYQRDGPMCMMDNQGGAPNYYPNSFSAPEHQPSALEHRTHFSGDVQRFNSANDDNVTQVRTFYLKVLNEEQRKRLCENIAGHLKDAQLFIQKKAVKNFSDVHPEYGSRIQALLDKYNE 501
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492         


Chain B from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......................eee.........hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh........ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeehhhhhhhh..................eeeeeeeeee...hhhhhh.............eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....................................hhhhh.........eee........hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkn B   3 NRDPASDQMKHWKEQRAAQKPDVLTTGGGNPVGDKLNSLTVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITRYSKAKVFEHIGKRTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDALLFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLAHEDPDYGLRDLFNAIATGNYPSWTLYIQVMTFSEAEIFPFNPFDLTKVWPHGDYPLIPVGKLVLNRNPVNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFAYPDTHRHRLGPNYLQIPVNCPYRARVANYQRDGPMCMMDNQGGAPNYYPNSFSAPEHQPSALEHRTHFSGDVQRFNSANDDNVTQVRTFYLKVLNEEQRKRLCENIAGHLKDAQLFIQKKAVKNFSDVHPEYGSRIQALLDKYNE 501
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492         


Chain C from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.......................eee.........hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeee......eeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh........ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeeehhhhhhh..................eeeeeeeeee...hhhhhh.............eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....................................hhhhh....eeeeeeee........hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkn C   3 NRDPASDQMKHWKEQRAAQKPDVLTTGGGNPVGDKLNSLTVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITRYSKAKVFEHIGKRTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDALLFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLAHEDPDYGLRDLFNAIATGNYPSWTLYIQVMTFSEAEIFPFNPFDLTKVWPHGDYPLIPVGKLVLNRNPVNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFAYPDTHRHRLGPNYLQIPVNCPYRARVANYQRDGPMCMMDNQGGAPNYYPNSFSAPEHQPSALEHRTHFSGDVQRFNSANDDNVTQVRTFYLKVLNEEQRKRLCENIAGHLKDAQLFIQKKAVKNFSDVHPEYGSRIQALLDKYNE 501
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492         


Chain D from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......................eee.........hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeehhhhhhh...................eeeeeeeeee...hhhhhh.............eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....................................hhhhh....eeeeeeee........hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkn D   3 NRDPASDQMKHWKEQRAAQKPDVLTTGGGNPVGDKLNSLTVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEVTHDITRYSKAKVFEHIGKRTPIAVRFSTVAGESGSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDALLFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLAHEDPDYGLRDLFNAIATGNYPSWTLYIQVMTFSEAEIFPFNPFDLTKVWPHGDYPLIPVGKLVLNRNPVNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFAYPDTHRHRLGPNYLQIPVNCPYRARVANYQRDGPMCMMDNQGGAPNYYPNSFSAPEHQPSALEHRTHFSGDVQRFNSANDDNVTQVRTFYLKVLNEEQRKRLCENIAGHLKDAQLFIQKKAVKNFSDVHPEYGSRIQALLDKYNE 501
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
   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 5GKN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GKN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GKN)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATA_BOVIN | P00432: 1tgu 1th2 1th3 1th4 3j7b 3nwl 3re8 3rgp 3rgs 4blc 7cat 8cat

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GKN)