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(-) Description

Title :  PYRUVATE OXIDASE VARIANT F479W IN COMPLEX WITH REACTION INTERMEDIATE 2-ACETYL-THIAMIN DIPHOSPHATE
 
Authors :  G. Wille, D. Meyer, A. Steinmetz, E. Hinze, R. Golbik, K. Tittmann
Date :  10 Nov 05  (Deposition) - 25 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tpp Enzyme, Reaction Intermediate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Wille, D. Meyer, A. Steinmetz, E. Hinze, R. Golbik, K. Tittmann
The Catalytic Cycle Of A Thiamin Diphosphate Enzyme Examine By Cryocrystallography.
Nat. Chem. Biol. V. 2 324 2006
PubMed-ID: 16680160  |  Reference-DOI: 10.1038/NCHEMBIO788

(-) Compounds

Molecule 1 - PYRUVATE OXIDASE
    ChainsA, B
    EC Number1.2.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBP200
    Expression System StrainC600
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePOX5
    MutationYES
    Organism ScientificLACTOBACILLUS PLANTARUM
    Organism Taxid1590
    SynonymPYRUVIC OXIDASE, POX

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2HTL2Ligand/Ion2-ACETYL-THIAMINE DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION
5PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2HTL4Ligand/Ion2-ACETYL-THIAMINE DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:447 , ASN A:474 , GLN A:476 , HTL A:1614 , HOH A:2095BINDING SITE FOR RESIDUE MG A 1610
02AC2SOFTWAREMET B:452 , GLN B:455 , HOH B:1687BINDING SITE FOR RESIDUE NA B 1611
03AC3SOFTWAREASP B:447 , ASN B:474 , GLN B:476 , HTL B:1617 , HOH B:1629BINDING SITE FOR RESIDUE MG B 1612
04AC4SOFTWAREMET A:452 , GLN A:455 , HOH A:1689BINDING SITE FOR RESIDUE NA A 1613
05AC5SOFTWAREPRO A:33 , GLU A:59 , SER A:82 , PRO A:85 , HIS A:89 , GLN A:122 , VAL A:394 , ASP A:396 , ALA A:420 , MET A:422 , GLY A:446 , ASP A:447 , GLY A:448 , GLY A:449 , ASN A:474 , GLN A:476 , TYR A:477 , GLY A:478 , TRP A:479 , ILE A:480 , MG A:1610 , HOH A:1618 , HOH A:1649 , HOH A:1652 , HOH A:2095BINDING SITE FOR RESIDUE HTL A 1614
06AC6SOFTWAREHIS A:101 , PHE A:121 , GLY A:220 , ILE A:221 , GLY A:222 , THR A:244 , TYR A:245 , ALA A:262 , ASN A:263 , ARG A:264 , VAL A:265 , GLY A:284 , ASN A:285 , ASN A:286 , TYR A:287 , PRO A:288 , PHE A:289 , ASP A:306 , ILE A:307 , ASP A:308 , LYS A:311 , ALA A:324 , ASP A:325 , ALA A:326 , ASN A:398 , SER A:416 , ASN A:417 , HOH A:1633 , HOH A:1648 , HOH A:1663 , HOH A:1682 , HOH A:1910BINDING SITE FOR RESIDUE FAD A 1615
07AC7SOFTWARELEU A:555 , LEU A:557 , ASP A:558 , MET A:561 , SER A:562 , HOH A:1816 , HOH A:1831BINDING SITE FOR RESIDUE PYR A 1616
08AC8SOFTWAREPRO B:33 , GLU B:59 , SER B:82 , PRO B:85 , HIS B:89 , GLN B:122 , VAL B:394 , ASP B:396 , ALA B:420 , MET B:422 , GLY B:446 , ASP B:447 , GLY B:448 , GLY B:449 , ASN B:474 , GLN B:476 , TYR B:477 , GLY B:478 , TRP B:479 , ILE B:480 , MG B:1612 , HOH B:1623 , HOH B:1629 , HOH B:1650 , HOH B:1658 , HOH B:1965BINDING SITE FOR RESIDUE HTL B 1617
09AC9SOFTWAREHIS B:101 , PHE B:121 , GLY B:220 , ILE B:221 , GLY B:222 , THR B:244 , TYR B:245 , ALA B:262 , ASN B:263 , ARG B:264 , VAL B:265 , GLY B:284 , ASN B:285 , ASN B:286 , TYR B:287 , PRO B:288 , PHE B:289 , ASP B:306 , ILE B:307 , ASP B:308 , LYS B:311 , ALA B:324 , ASP B:325 , ALA B:326 , ASN B:398 , SER B:416 , ASN B:417 , HOH B:1638 , HOH B:1639 , HOH B:1670 , HOH B:1679 , HOH B:1981 , HOH B:2080BINDING SITE FOR RESIDUE FAD B 1618
10BC1SOFTWARELEU B:555 , ARG B:556 , LEU B:557 , ASP B:558 , MET B:561 , SER B:562 , HOH B:1962BINDING SITE FOR RESIDUE PYR B 1619

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EZU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.POXB_LACPL430-449
 
  2A:430-449
B:430-449
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.POXB_LACPL430-449
 
  4A:430-449
B:430-449

(-) Exons   (0, 0)

(no "Exon" information available for 2EZU)

(-) 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:585
 aligned with POXB_LACPL | P37063 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:585
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588     
           POXB_LACPL     9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSATSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
               SCOP domains d2ezua2 A:9-182 automated matches                                                                                                                                             d2ezua1 A:183-365 Pyruvate oxidase                                                                                                                                                     d2ezua3 A:366-593 automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2ezuA01 A:9-192  [code=3.40.50.970, no name defined]                                                                                                                                    2ezuA02 A:193-359 TPP-binding domain                                                                                                                                   2ezuA03 A:360-549  [code=3.40.50.970, no name defined]                                                                                                                                        -------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhh....eeee.....hhhhhhhhhhhhhhhh..eeeeeee.hhhh.eee......hhhhh........hhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhhh..eee.hhhh..................hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhh..hhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhhh.....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezu A   9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGWIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588     

Chain B from PDB  Type:PROTEIN  Length:585
 aligned with POXB_LACPL | P37063 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:585
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588     
           POXB_LACPL     9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSATSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
               SCOP domains d2ezub2 B:9-182 automated matches                                                                                                                                             d2ezub1 B:183-365 Pyruvate oxidase                                                                                                                                                     d2ezub3 B:366-593 automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2ezuB01 B:9-192  [code=3.40.50.970, no name defined]                                                                                                                                    2ezuB02 B:193-359 TPP-binding domain                                                                                                                                   2ezuB03 B:360-549  [code=3.40.50.970, no name defined]                                                                                                                                        -------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh.eeeeeee.hhhh.eee......hhhhh........hhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhhh..eee.hhhh.........eeee.....hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhh......hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezu B   9 TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRHEEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALIGQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGWIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD 593
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588     

   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  (2, 6)

Asymmetric Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POXB_LACPL | P37063)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) 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:0047112    pyruvate oxidase activity    Catalysis of the reaction: H(+) + O(2) + phosphate + pyruvate = acetyl phosphate + CO(2) + H(2)O(2).
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POXB_LACPL | P370631pow 1pox 1y9d 2ez4 2ez8 2ez9 2ezt

(-) Related Entries Specified in the PDB File

1pow PYRUVATE OXIDASE WILD-TYPE
1pox PYRUVATE OXIDASE, STABILIZED MUTANT
1y9d PYRUVATE OXIDASE VARIANT V265A
2ez4
2ez8
2ez9
2ezt