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(-) Description

Title :  CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE FROM ESCHERICHIA COLI IN COMPLEX WITH ADENOSINE-5`-DIPHOSPHATE
 
Authors :  T. Werther, A. Zimmer, G. Wille, G. Hubner, M. S. Weiss, S. Konig
Date :  26 May 07  (Deposition) - 03 Jun 08  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase; Oxalyl-Coa Decarboxylase; Oxalate Degradation; Thiamine Diphosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Werther, A. Zimmer, G. Wille, R. Golbik, M. S. Weiss, S. Konig
New Insights Into Structure-Function Relationships Of Oxaly Coa Decarboxylase From Escherichia Coli.
Febs J. V. 277 2628 2010
PubMed-ID: 20553497  |  Reference-DOI: 10.1111/J.1742-464X.2010.07673.X

(-) Compounds

Molecule 1 - OXALYL-COA DECARBOXYLASE
    ChainsA, B
    EC Number4.1.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMS470-115/6/5
    Expression System StrainBL21
    Expression System Vector TypePLASMID
    GeneYFDU
    Organism ScientificESCHERICHIA COLI
    StrainK-12

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG2Ligand/IonMAGNESIUM ION
5SO42Ligand/IonSULFATE ION
6TPP2Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (5, 24)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5SO44Ligand/IonSULFATE ION
6TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:447 , ASN A:474 , GLY A:476 , HOH A:4057BINDING SITE FOR RESIDUE MG A 1001
02AC2SOFTWAREASP B:447 , ASN B:474 , GLY B:476 , HOH B:5088BINDING SITE FOR RESIDUE MG B 1002
03AC3SOFTWARETYR A:118 , TYR A:478 , SER A:550 , HOH A:4085 , HOH A:4115 , HOH A:4174 , HOH A:4371 , HOH A:4467BINDING SITE FOR RESIDUE SO4 A 2001
04AC4SOFTWARETYR B:118 , TYR B:478 , SER B:550 , HOH B:5158 , HOH B:5171 , HOH B:5302 , HOH B:5373BINDING SITE FOR RESIDUE SO4 B 2002
05AC5SOFTWAREGLU A:54 , PRO A:80 , ASN A:84 , TYR A:372 , GLY A:395 , ALA A:396 , ASN A:397 , THR A:398 , GLY A:421 , MET A:423 , GLY A:446 , ASP A:447 , SER A:448 , ALA A:449 , PHE A:452 , ASN A:474 , GLY A:476 , ILE A:477 , TYR A:478 , HOH A:4057 , HOH A:4174BINDING SITE FOR RESIDUE TPP A 4001
06AC6SOFTWAREARG A:158 , GLY A:219 , LYS A:220 , GLY A:221 , TYR A:224 , MET A:245 , GLY A:278 , ALA A:279 , ARG A:280 , LEU A:284 , ASP A:302 , ILE A:303 , GLY A:320 , ASP A:321 , ILE A:322 , HOH A:4029 , HOH A:4031 , HOH A:4052 , HOH A:4072 , HOH A:4272BINDING SITE FOR RESIDUE ADP A 4003
07AC7SOFTWAREILE A:32 , PRO A:33 , THR A:35 , ASP A:36 , GLU A:549 , SER A:550 , GLY A:551 , HIS A:552 , ILE A:553 , HOH A:4080 , HOH A:4216BINDING SITE FOR RESIDUE MES A 4004
08AC8SOFTWAREGLU B:54 , PRO B:80 , ASN B:84 , TYR B:372 , GLY B:395 , ALA B:396 , ASN B:397 , THR B:398 , GLY B:421 , MET B:423 , GLY B:446 , ASP B:447 , SER B:448 , ALA B:449 , PHE B:452 , ASN B:474 , GLY B:476 , ILE B:477 , TYR B:478 , HOH B:5088 , HOH B:5302BINDING SITE FOR RESIDUE TPP B 5001
09AC9SOFTWAREARG B:158 , GLY B:219 , LYS B:220 , GLY B:221 , MET B:245 , GLY B:278 , ALA B:279 , ARG B:280 , LEU B:284 , ASP B:302 , ILE B:303 , GLU B:304 , GLY B:320 , ASP B:321 , ILE B:322 , HOH B:5026 , HOH B:5038 , HOH B:5066 , HOH B:5068 , HOH B:5322BINDING SITE FOR RESIDUE ADP B 5003
10BC1SOFTWAREILE B:32 , PRO B:33 , THR B:35 , ASP B:36 , GLU B:549 , SER B:550 , GLY B:551 , HIS B:552 , ILE B:553 , HOH B:5086 , HOH B:5424BINDING SITE FOR RESIDUE MES B 5004
11BC2SOFTWAREASN A:95 , GLY A:96 , PHE A:97 , PRO A:159 , LYS A:220 , GLY A:221 , TYR A:224 , HOH A:4093BINDING SITE FOR RESIDUE EDO A 3001
12BC3SOFTWAREASN B:95 , GLY B:96 , PHE B:97 , PRO B:159 , LYS B:220 , TYR B:224 , HOH B:5079BINDING SITE FOR RESIDUE EDO B 3002
13BC4SOFTWAREGLN A:115 , HIS A:287 , LYS A:289 , ASN A:311 , HOH A:4062 , HOH A:4135 , HOH A:4187 , HOH A:4230BINDING SITE FOR RESIDUE EDO A 3003
14BC5SOFTWAREHOH A:4297 , THR B:182 , THR B:183 , HOH B:5025 , HOH B:5296 , HOH B:5420BINDING SITE FOR RESIDUE EDO B 3004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q28)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:32 -Pro A:33
2Gln A:368 -Pro A:369
3Ile B:32 -Pro B:33
4Gln B:368 -Pro B:369

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q28)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q28)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q28)

(-) 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:550
 aligned with OXC_ECOLI | P0AFI0 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:550
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554
            OXC_ECOLI     5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTESGHIT 554
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhheeehhhhhhh..........eeehhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee.hhhh..........hhhhhhhhhhhh.eeeee....hhhhhhhh.......eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee...........................hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..eeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q28 A   5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTESGHIT 554
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554

Chain B from PDB  Type:PROTEIN  Length:550
 aligned with OXC_ECOLI | P0AFI0 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:550
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554
            OXC_ECOLI     5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTESGHIT 554
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TPP_enzyme_N-2q28B05 B:8-179                                                                                                                                                ---------------------TPP_enzyme_M-2q28B01 B:201-329                                                                                                   ----------------------------------------------------------------TPP_enzyme_C-2q28B03 B:394-540                                                                                                                     -------------- Pfam domains (1)
           Pfam domains (2) ---TPP_enzyme_N-2q28B06 B:8-179                                                                                                                                                ---------------------TPP_enzyme_M-2q28B02 B:201-329                                                                                                   ----------------------------------------------------------------TPP_enzyme_C-2q28B04 B:394-540                                                                                                                     -------------- Pfam domains (2)
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhheeehhhhhhh..........eeehhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee.hhhh..........hhhhhhhhhhhh.eeeee....hhhhhhhh.......eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee...........................hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..eeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q28 B   5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTESGHIT 554
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554

   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 2Q28)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q28)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: FAD_DHS (82)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (OXC_ECOLI | P0AFI0)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008949    oxalyl-CoA decarboxylase activity    Catalysis of the reaction: H(+) + oxalyl-CoA = CO(2) + formyl-CoA.
    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:0071468    cellular response to acidic pH    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0033611    oxalate catabolic process    The chemical reactions and pathways resulting in the breakdown of oxalate, the organic acid ethanedioate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OXC_ECOLI | P0AFI02q27 2q29

(-) Related Entries Specified in the PDB File

2q27 2q29